library(readr)
library(ggplot2)
library(lattice)
library(ggridges)
library(ggvis)
## 
## Attaching package: 'ggvis'
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##     resolution
library(ggthemes)
library(cowplot)
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## Attaching package: 'cowplot'
## The following object is masked from 'package:ggthemes':
## 
##     theme_map
library(gapminder)
library(gganimate)
## No renderer backend detected. gganimate will default to writing frames to separate files
## Consider installing:
## - the `gifski` package for gif output
## - the `av` package for video output
## and restarting the R session
## 
## Attaching package: 'gganimate'
## The following object is masked from 'package:ggvis':
## 
##     view_static
library(dplyr)
## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
library(tidyverse)
## ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2
## ──
## ✔ tibble  3.1.8     ✔ stringr 1.5.0
## ✔ tidyr   1.3.0     ✔ forcats 1.0.0
## ✔ purrr   1.0.1     
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter()     masks stats::filter()
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library(grid)
library(gridExtra)
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## Attaching package: 'gridExtra'
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##     combine
library(RColorBrewer)
library(readr)
#Covid-liver cancer Example
Cancer<- read_csv("~/Downloads/Breast_Cancer.csv")
## Rows: 379 Columns: 7
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): Survivor, Stage
## dbl (5): Age, Tumor Size, Regional Node Examined, Reginol Node Positive, Sur...
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Cancer
## # A tibble: 379 × 7
##    Survivor   Age Stage `Tumor Size` `Regional Node Examined` Reginol …¹ Survi…²
##    <chr>    <dbl> <chr>        <dbl>                    <dbl>      <dbl>   <dbl>
##  1 Alive       68 T1               4                       24          1      60
##  2 Alive       50 T2              35                       14          5      62
##  3 Alive       58 T3              63                       14          7      75
##  4 Alive       58 T1              18                        2          1      84
##  5 Alive       47 T2              41                        3          1      50
##  6 Alive       51 T1              20                       18          2      89
##  7 Alive       51 T1               8                       11          1      54
##  8 Dead        40 T2              30                        9          1      14
##  9 Alive       40 T4             103                       20         18      70
## 10 Alive       69 T4              32                       21         12      92
## # … with 369 more rows, and abbreviated variable names
## #   ¹​`Reginol Node Positive`, ²​`Survival Months`
str(Cancer)
## spc_tbl_ [379 × 7] (S3: spec_tbl_df/tbl_df/tbl/data.frame)
##  $ Survivor              : chr [1:379] "Alive" "Alive" "Alive" "Alive" ...
##  $ Age                   : num [1:379] 68 50 58 58 47 51 51 40 40 69 ...
##  $ Stage                 : chr [1:379] "T1" "T2" "T3" "T1" ...
##  $ Tumor Size            : num [1:379] 4 35 63 18 41 20 8 30 103 32 ...
##  $ Regional Node Examined: num [1:379] 24 14 14 2 3 18 11 9 20 21 ...
##  $ Reginol Node Positive : num [1:379] 1 5 7 1 1 2 1 1 18 12 ...
##  $ Survival Months       : num [1:379] 60 62 75 84 50 89 54 14 70 92 ...
##  - attr(*, "spec")=
##   .. cols(
##   ..   Survivor = col_character(),
##   ..   Age = col_double(),
##   ..   Stage = col_character(),
##   ..   `Tumor Size` = col_double(),
##   ..   `Regional Node Examined` = col_double(),
##   ..   `Reginol Node Positive` = col_double(),
##   ..   `Survival Months` = col_double()
##   .. )
##  - attr(*, "problems")=<externalptr>
#Get the Correlations between the measurements

Cancer$Stage<-as.numeric(factor(Cancer$Stage, labels=c("1","2","3","4")))
Cancer1=cor(Cancer[-1])
colMeans(Cancer1)
##                    Age                  Stage             Tumor Size 
##             0.08831564             0.32741868             0.32781241 
## Regional Node Examined  Reginol Node Positive        Survival Months 
##             0.25464267             0.31035610             0.10189760
library (ggplot2)
ggplot(Cancer, aes(x=Stage, fill=Survivor))+geom_boxplot()+ labs(title='Survivorship comparison')

ggplot(Cancer, aes(x=Survivor,y=Stage)) + geom_boxplot()

# Using prcomp to compute the principal components (eigenvalues and eigenvectors). With scale=TRUE, variable means are set to zero, and variances set to one
Cancer_pca <- prcomp(Cancer[,-1],scale=TRUE)
Cancer_pca
## Standard deviations (1, .., p=6):
## [1] 1.4959541 1.0793515 0.9891605 0.9596806 0.7141874 0.4331658
## 
## Rotation (n x k) = (6 x 6):
##                               PC1         PC2         PC3         PC4
## Age                    -0.2153849  0.21608166 -0.34917081 -0.88535662
## Stage                   0.5628689 -0.32693628  0.06177527 -0.24457235
## Tumor Size              0.5822135 -0.28223117 -0.01433325 -0.21375444
## Regional Node Examined  0.2375181  0.75305159  0.21117279  0.02093686
## Reginol Node Positive   0.4590407  0.43924020  0.01680220  0.01827332
## Survival Months        -0.1751633 -0.08214803  0.91059423 -0.33145859
##                                PC5          PC6
## Age                    -0.03346239  0.004663803
## Stage                   0.18847337  0.690751203
## Tumor Size              0.13490974 -0.719218983
## Regional Node Examined  0.57570300 -0.005676451
## Reginol Node Positive  -0.77028208  0.048979548
## Survival Months        -0.14279002 -0.055980895
summary(Cancer_pca)
## Importance of components:
##                          PC1    PC2    PC3    PC4     PC5     PC6
## Standard deviation     1.496 1.0794 0.9892 0.9597 0.71419 0.43317
## Proportion of Variance 0.373 0.1942 0.1631 0.1535 0.08501 0.03127
## Cumulative Proportion  0.373 0.5672 0.7302 0.8837 0.96873 1.00000
# sample scores stored in sparrows_pca$x
# singular values (square roots of eigenvalues) stored in sparrow_pca$sdev
# loadings (eigenvectors) are stored in sparrows_pca$rotation
# variable means stored in sparrows_pca$center
# variable standard deviations stored in sparrows_pca$scale
# A table containing eigenvalues and %'s accounted, follows
# Eigenvalues are sdev^2
(eigen_Cancer <- Cancer_pca$sdev^2)
## [1] 2.2378787 1.1649997 0.9784385 0.9209868 0.5100636 0.1876326
names(eigen_Cancer) <- paste("PC",1:5,sep="")
eigen_Cancer
##       PC1       PC2       PC3       PC4       PC5      <NA> 
## 2.2378787 1.1649997 0.9784385 0.9209868 0.5100636 0.1876326
sumlambdas <- sum(eigen_Cancer)
sumlambdas
## [1] 6
propvar <- eigen_Cancer/sumlambdas
propvar
##        PC1        PC2        PC3        PC4        PC5       <NA> 
## 0.37297979 0.19416662 0.16307309 0.15349780 0.08501061 0.03127210
cumvar_Cancer <- cumsum(propvar)
cumvar_Cancer
##       PC1       PC2       PC3       PC4       PC5      <NA> 
## 0.3729798 0.5671464 0.7302195 0.8837173 0.9687279 1.0000000
matlambdas <- rbind(eigen_Cancer,propvar,cumvar_Cancer)
rownames(matlambdas) <- c("Eigenvalues","Prop. variance","Cum. prop. variance")
round(matlambdas,4)
##                        PC1    PC2    PC3    PC4    PC5   <NA>
## Eigenvalues         2.2379 1.1650 0.9784 0.9210 0.5101 0.1876
## Prop. variance      0.3730 0.1942 0.1631 0.1535 0.0850 0.0313
## Cum. prop. variance 0.3730 0.5671 0.7302 0.8837 0.9687 1.0000
summary(Cancer_pca)
## Importance of components:
##                          PC1    PC2    PC3    PC4     PC5     PC6
## Standard deviation     1.496 1.0794 0.9892 0.9597 0.71419 0.43317
## Proportion of Variance 0.373 0.1942 0.1631 0.1535 0.08501 0.03127
## Cumulative Proportion  0.373 0.5672 0.7302 0.8837 0.96873 1.00000
Cancer_pca$rotation
##                               PC1         PC2         PC3         PC4
## Age                    -0.2153849  0.21608166 -0.34917081 -0.88535662
## Stage                   0.5628689 -0.32693628  0.06177527 -0.24457235
## Tumor Size              0.5822135 -0.28223117 -0.01433325 -0.21375444
## Regional Node Examined  0.2375181  0.75305159  0.21117279  0.02093686
## Reginol Node Positive   0.4590407  0.43924020  0.01680220  0.01827332
## Survival Months        -0.1751633 -0.08214803  0.91059423 -0.33145859
##                                PC5          PC6
## Age                    -0.03346239  0.004663803
## Stage                   0.18847337  0.690751203
## Tumor Size              0.13490974 -0.719218983
## Regional Node Examined  0.57570300 -0.005676451
## Reginol Node Positive  -0.77028208  0.048979548
## Survival Months        -0.14279002 -0.055980895
print(Cancer_pca)
## Standard deviations (1, .., p=6):
## [1] 1.4959541 1.0793515 0.9891605 0.9596806 0.7141874 0.4331658
## 
## Rotation (n x k) = (6 x 6):
##                               PC1         PC2         PC3         PC4
## Age                    -0.2153849  0.21608166 -0.34917081 -0.88535662
## Stage                   0.5628689 -0.32693628  0.06177527 -0.24457235
## Tumor Size              0.5822135 -0.28223117 -0.01433325 -0.21375444
## Regional Node Examined  0.2375181  0.75305159  0.21117279  0.02093686
## Reginol Node Positive   0.4590407  0.43924020  0.01680220  0.01827332
## Survival Months        -0.1751633 -0.08214803  0.91059423 -0.33145859
##                                PC5          PC6
## Age                    -0.03346239  0.004663803
## Stage                   0.18847337  0.690751203
## Tumor Size              0.13490974 -0.719218983
## Regional Node Examined  0.57570300 -0.005676451
## Reginol Node Positive  -0.77028208  0.048979548
## Survival Months        -0.14279002 -0.055980895
## Sample scores stored in sparrow_pca$x
Cancer_pca$x
##                 PC1          PC2          PC3          PC4          PC5
##   [1,] -1.493744354  1.672703734 -0.797771118 -0.639380539  0.852277723
##   [2,]  0.426322428 -0.124086338 -0.222112841  0.478038848 -0.014925567
##   [3,]  1.694207768 -0.545124348  0.069937198 -1.032701826 -0.039058417
##   [4,] -1.767583528 -0.885302494 -0.030847119 -0.208720400 -0.771910136
##   [5,]  0.043714825 -1.603388200 -0.903121553  0.849669634 -0.078371793
##   [6,] -1.028534021  0.502739380  0.863904840  0.421284750  0.233248754
##   [7,] -1.338771984  0.023023987 -0.740136022  1.021953281  0.038121315
##   [8,]  0.406514411 -0.944219552 -1.935001240  2.169992691  0.548288673
##   [9,]  4.993025728 -0.305103355  0.801778453  0.176933443 -0.724303190
##  [10,]  1.937948477  0.689507346  0.639790414 -2.348269489 -0.376692694
##  [11,] -1.756901401  0.140915113 -1.036789014 -0.816405788 -0.204199065
##  [12,]  1.296312778 -1.473829054  1.127778467 -0.112920985  0.266696937
##  [13,] -0.090142691 -0.016296775 -1.070302648 -0.891412586  0.200775716
##  [14,] -0.076244034  1.581531699 -0.943407970  1.540387096  0.141353261
##  [15,]  1.004107956  1.120512340 -0.515080564 -0.672554789 -1.296448032
##  [16,] -1.005634503  0.998331229 -1.092830786  0.057925043  0.742413832
##  [17,] -0.538374841 -1.839056096  0.934166263 -0.882076640 -0.578346113
##  [18,]  0.204445317  0.244548369  0.249012257  1.256474649  1.134795943
##  [19,] -0.419443766 -0.379535399  1.728764442  0.083365143  0.402986436
##  [20,] -0.252782392  0.344103196  0.155613436 -0.655869450  0.860603335
##  [21,] -0.036353656 -0.349284099  0.645811404  0.425442619  0.372107468
##  [22,]  0.504291512  0.121502823 -0.952996651 -0.061329141  0.135596833
##  [23,] -0.618672209 -1.285043286 -0.036105811 -0.229784303 -0.280109421
##  [24,]  1.459334722 -1.104003050  1.630015919 -0.538883137  1.064729564
##  [25,]  0.693501261  3.217631237  1.088615995 -0.680914229 -2.330312186
##  [26,]  1.342457422  2.945510521  0.104659090 -0.694326558 -0.785747318
##  [27,]  2.475721782  2.107120006  1.821692902  0.042150966 -2.125689786
##  [28,] -1.137184838 -0.018509243  0.662500068  1.019754895  0.143564512
##  [29,] -0.082096727  0.062026127 -0.404849247 -0.143815038  0.043817854
##  [30,] -0.951459346 -0.397603334  0.033425845 -1.324785280  0.016907630
##  [31,]  0.004306142 -1.599200390 -0.821234717  0.828802331 -0.096628489
##  [32,] -1.358590305 -0.557530387 -1.182191573  0.826013095 -0.330970546
##  [33,] -1.790419403 -0.472260893  0.282426323 -0.357402908 -0.542183270
##  [34,] -0.908445651  0.994824271 -0.546660828 -0.042005466  0.292432820
##  [35,]  1.245709794  0.857794242 -1.178327309  1.397760831 -0.230660457
##  [36,] -1.439873416 -0.186081367  0.144133667  0.662537801 -0.393665514
##  [37,]  0.636390371  0.900377415 -1.197745317  0.553485818  0.437914429
##  [38,] -1.304428696  0.097530771  1.328492259  0.221100925 -0.155155562
##  [39,] -0.097417933 -0.858136005  0.513336501  0.257353363  0.029439452
##  [40,] -0.188925650 -0.025716107  1.521237025 -0.147451873 -0.286733286
##  [41,]  2.535953943 -0.283072938 -1.273811462 -0.496124138 -0.691155605
##  [42,] -1.364589888  0.380987232 -0.926166470 -0.409214549 -0.084453563
##  [43,] -1.095258604 -1.245692755 -0.025636708 -0.959504567 -0.544787256
##  [44,]  0.018958421  0.185171532  0.594724325 -0.026225609 -0.312285920
##  [45,] -1.483766860  0.205593899 -0.521531513  0.532329976 -0.202487124
##  [46,]  0.803570710 -0.823728790  0.269737583 -1.940110944 -0.213877418
##  [47,] -0.776759752  0.318065419 -0.898736044  2.118307298  0.308120927
##  [48,] -1.440160549  0.277491231 -0.933452622 -0.172656258  0.076695703
##  [49,]  0.550199236  0.443259288  0.544534206 -0.061726221 -0.634281043
##  [50,] -1.959716237  0.269905907 -0.358261698 -1.104900464 -0.742921582
##  [51,]  0.283946083 -0.215989222  0.718462913  1.705505213  0.429398197
##  [52,]  0.584420507 -1.170636855 -0.658910102 -2.000608348  0.454750957
##  [53,]  2.164109035 -2.375151885  0.202704168 -1.926001263  0.605914036
##  [54,]  1.673683848 -0.438611018 -0.189966395 -1.566014043  1.244480037
##  [55,] -1.630123732  0.631351549 -0.019980046  0.212113815  0.215871580
##  [56,] -1.450559221  0.201501035 -0.069005014  0.333630589  0.063005452
##  [57,] -0.534036352  0.291756051  0.624478817 -1.023860005  0.669994233
##  [58,] -0.354843129  3.274197111  2.410035980  0.361353654  2.502769179
##  [59,] -1.178588655  0.226034827  0.171909908  0.786762124  0.247357475
##  [60,] -1.248535425  0.638963394  0.202025885  0.279803670  0.179044984
##  [61,] -0.944827480  1.241989527  0.467351263  0.104831170  0.693575290
##  [62,] -1.056029210  0.031887224 -0.922233051  1.020017722  0.191600412
##  [63,] -0.473763736 -1.839525046  0.381440310  1.043813308 -0.465299021
##  [64,]  1.681009012 -0.528168820  0.166784745 -1.236306623  1.216190250
##  [65,] -1.312786276  0.965097163 -0.969708882 -0.635102168  0.024970627
##  [66,] -1.639877002 -0.931529988  1.401477586  0.658502060 -0.668767345
##  [67,]  4.455166578  1.087532562  0.124772958  2.053348449 -1.489900944
##  [68,] -0.707613499  0.590986037  1.179291019  1.595111891  0.263308423
##  [69,] -1.710632794 -0.549715482 -0.153074842 -0.100695874 -0.540451474
##  [70,] -1.171903123  0.100583865  0.469100757  0.412780064 -0.339388614
##  [71,]  3.302612150 -1.737283578  1.502810946 -1.179097587 -0.118238924
##  [72,]  2.121655213  2.644141124 -2.473204090 -0.044893038 -1.314192531
##  [73,]  0.528823585 -0.636078944  0.137430927  2.495082814  0.843161685
##  [74,] -1.868775707  0.569029628  0.581800057 -1.084485611  0.002065102
##  [75,]  0.683905846  1.767290796  0.241693051 -1.337566812 -1.608284497
##  [76,]  0.821006546 -1.188104492  0.917466077 -1.089980478  0.637354405
##  [77,] -0.499967072 -0.063567628 -0.217092609 -1.242667319 -0.300754296
##  [78,]  0.056071716 -1.653376800  1.664161542  0.435774870 -0.079376450
##  [79,]  0.099588612 -1.161140621  0.358003056 -0.058098223  0.191212303
##  [80,] -1.638985742  0.150875793 -1.403816856 -0.700686152 -0.135813445
##  [81,]  0.865297254  1.214733944  1.463461173 -0.297882350 -1.014695877
##  [82,] -1.545124764  0.127252910 -0.935729044 -0.793110208 -0.096332740
##  [83,] -0.757282603 -0.365269832 -0.559376514 -1.125365040 -0.112495907
##  [84,] -1.494668798 -0.862217669 -1.017557513  0.729371690 -0.585327071
##  [85,] -1.198962297  0.090483632 -0.244225721  0.803338834  0.150630291
##  [86,]  1.053228198  0.023027292  0.260206980  0.703883631 -1.086933498
##  [87,]  2.839883593 -2.296312935  0.510353279 -0.693661524  0.066738128
##  [88,]  1.506058603 -1.812772768  0.528733408 -0.767001468  0.643656650
##  [89,] -1.539415867 -0.136768478  0.768955037 -0.049503375 -0.188258747
##  [90,] -2.166532837  0.071753733  0.343483494 -0.898166612 -0.445936393
##  [91,]  0.893002750 -1.772886261  0.734063638 -0.797845672  0.341156668
##  [92,] -0.677904182 -0.104397875  0.169469929  2.673756815  0.405882517
##  [93,] -0.646604416 -0.740495104  0.063231982 -1.095809541 -0.767513218
##  [94,]  1.683330979  1.567742424 -0.698706197  1.431672587 -1.080548515
##  [95,] -1.509921397  0.297490480  0.490010821 -0.323083740 -0.437095352
##  [96,] -0.135237286  0.293266912 -1.015571227 -0.225694168  0.642455326
##  [97,]  0.027644129 -1.133291443 -1.997458759  1.032137750 -0.070625404
##  [98,] -0.637273583 -0.513850978 -0.306967375 -0.684532247  0.140054208
##  [99,]  1.070049729 -2.036508976 -0.316339810 -0.094341352 -0.094161935
## [100,] -0.455435814  0.089328755 -1.403983913 -1.027093674  0.560281943
## [101,]  4.600390311  2.244846920  0.532264308  1.259266636 -1.010942778
## [102,] -0.787145836  1.086091949  0.549806202  1.093912587  0.984179992
## [103,]  0.655142324 -1.683984928 -2.308143986  2.208715115  0.240582243
## [104,] -0.428540034 -0.840500324 -1.048098702 -0.027665882  0.077046929
## [105,] -0.110654721 -0.123171275 -0.175937919  0.338031509  0.196792323
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## [300,]  1.238726422 -0.682019739 -1.206227105 -1.584533216  0.599257188
## [301,]  0.476798036 -0.538294379  1.306977504  0.589987890  0.804993508
## [302,]  0.451358041  0.509847268 -0.404959275  1.025191596  1.150524367
## [303,] -0.410664267  1.809811675  0.163254213  1.203959868  1.107465182
## [304,]  0.631511135  4.553878477  0.617849698 -0.258625983  0.452803511
## [305,]  0.606275351  1.307303704 -1.190130416 -1.085147986  0.839582865
## [306,]  3.760469200 -1.318016453 -1.571659239 -0.958198521 -0.168654341
## [307,]  0.283257978  0.334225557  0.900109850  1.387190281  0.742119351
## [308,]  1.205872572 -1.025116718 -0.694241491 -0.489820821  0.185091372
## [309,] -0.547890175 -1.378267017  0.199506501  0.006777245 -0.282776412
## [310,]  0.675442079 -0.040092847  0.040280714  1.538300103  0.724233244
## [311,] -0.347420655 -1.297275709 -0.084885546  0.216594996 -0.374740492
## [312,] -1.082694803  1.058501944 -1.274637266 -0.535652316 -0.301170989
## [313,] -0.809911038  0.678119879 -0.193503870  0.489931605 -0.567989774
## [314,]  2.814192996  1.465015414  1.296910650 -1.024401483 -0.754090861
## [315,] -1.219216145 -0.216402526  0.775638956  0.706433637 -0.029531003
## [316,] -0.839858529 -1.160921154 -0.067522123 -0.376613864 -0.332337533
## [317,]  1.906604890 -1.476681383 -0.028831221  0.037013607  1.083914038
## [318,] -1.128786006  0.395890021  0.040446729  0.390323605 -0.149885563
## [319,]  4.980287452  1.400993226  0.386980437  0.646687478 -1.083846603
## [320,] -0.396555408 -0.215395452 -1.222389233 -0.813225124  0.424557329
## [321,] -1.686147468  0.664222126  1.210799613 -0.375476795  0.198108774
## [322,] -0.771587552  0.001912498 -0.021523533  2.182231316  0.393142757
## [323,]  2.121003409 -2.080663494  0.161998088  0.897550000  0.380306029
## [324,]  0.183525269  0.711131176  0.676974276 -0.837925098 -0.201495035
## [325,] -0.388480855 -0.019183155 -0.034180507 -0.379134234  0.583222451
## [326,] -0.270374270  0.372642009  0.619830911 -1.148519958 -0.407017698
## [327,] -0.016309255 -0.272150173  1.123754077 -0.347941297 -0.103237180
## [328,] -1.509365115 -1.227221931  0.110956778  1.437386493 -0.758506439
## [329,]  1.128006246 -1.746278013  0.499382396 -1.619420542  0.555724903
## [330,] -0.013678857  0.097843119  0.408072714 -0.795855347 -1.175223096
## [331,]  0.134239505  0.261168839  1.687827776  0.217195174  1.082628063
## [332,]  0.543266130  0.289044087 -1.889627887  1.415180585  1.063577278
## [333,] -1.694510184 -0.384164773  0.978956440 -0.619188118 -0.943767153
## [334,] -1.177192240  0.755347480 -0.072837954  0.262273753  0.532730202
## [335,] -0.154704801 -0.482019591 -0.130393501  0.108703255  0.455787032
## [336,] -1.222393212 -0.140605864  0.470903440  0.854635087 -0.236602493
## [337,]  0.985284375 -2.085350193 -0.309169317 -0.356636930  0.209646403
## [338,]  1.845084419 -1.284127961 -0.428328294 -1.460289251  0.838247554
## [339,] -1.537001279  1.111570387  0.652894920 -1.060718845 -0.002140100
## [340,]  0.486580696 -0.438599188 -0.143918334  0.966749788  0.107166844
## [341,] -0.381846642 -0.365594889  0.626052636  0.039508221 -0.092159877
## [342,] -1.058469609  1.839970213 -0.254329772 -0.731552164 -0.827823834
## [343,]  1.953784231 -1.229071105  0.160259672  0.867246394  1.295990204
## [344,] -1.632770525 -0.310017947  0.586575867  0.624972262 -0.312659105
## [345,] -0.069211481  1.179578849 -0.019456868 -1.025693279  0.424192027
## [346,]  0.924645953  0.318200997 -0.038558980 -0.176342543 -1.278270521
## [347,] -1.679627649 -0.870249748  1.201962925  0.638583744 -0.657934688
## [348,] -0.138978457 -0.327879510  1.445999742  0.018109114  0.324021275
## [349,] -0.306354427  2.443421548  0.256738595  0.723881262  0.004780055
## [350,] -1.082397105  0.511694553  0.396630701  0.376171916  0.200267508
## [351,]  1.560087096 -0.172608049  2.042673531  0.001387343  0.943307040
## [352,]  0.213890453  0.121650120 -0.363220480  0.143134581  0.251009799
## [353,] -1.243101129 -0.469575151 -1.404226113  1.148855158 -0.206147146
## [354,] -1.723673624 -0.628891973  1.215101216  0.822337346 -0.530509884
## [355,] -1.845736715 -1.246640827  1.218806001  0.592440275 -0.970712299
## [356,] -0.533908899  0.509703545 -1.010222476 -1.067833304  0.770760459
## [357,] -0.621852817  1.060330174 -0.185420284  0.974853637  0.788314716
## [358,] -0.663822556 -0.698693563 -1.437208451 -1.000964685 -0.267520648
## [359,] -1.464448793 -0.997923794  0.090438438  0.991886193 -0.619748924
## [360,] -1.523194528  1.088366756 -0.015584201 -1.071387626  0.484479318
## [361,] -0.249284791 -0.495162923 -0.888175969  0.194375075  0.137323234
## [362,] -0.978278825  0.745196276  1.673492426  0.624652999  0.677279063
## [363,]  2.298810986 -0.090143085 -0.751106742 -0.561856912  1.569191798
## [364,] -0.641761160 -1.573225212  0.960424847 -0.179437036 -0.696431558
## [365,] -1.237501132 -0.412442737  1.793811573  1.137104529 -0.371283677
## [366,] -1.157403928  0.923508573 -0.442026074 -0.884941552 -0.171459484
## [367,] -0.796933393  1.222876039  0.723404723 -0.237384378 -0.510118334
## [368,]  2.646899548  0.301553970  0.690593527 -2.443750630  0.663805037
## [369,] -0.178975454 -0.138624086  1.105283992 -1.499072183 -0.164055484
## [370,] -1.330874437  0.769296425 -0.127097036 -1.223980155 -0.869663470
## [371,]  0.785519987  2.132318925  0.981263612 -0.639682484 -0.035075161
## [372,]  4.528600634 -0.995996130  0.568209680 -0.292649916 -0.397415282
## [373,] -2.215387412 -0.717213408  0.437807288 -1.098624561 -0.945243579
## [374,]  0.852816653  0.697424945 -0.415247520  0.859928559  0.964247801
## [375,]  1.528575274  1.579100810  0.424898608  1.740887715 -0.368739736
## [376,]  1.052831636  0.469776583  0.746395631 -0.477473960 -1.373515237
## [377,]  3.308075529 -0.637217047 -0.361014725 -0.281269186 -0.462933899
## [378,]  0.145308323 -0.337470348  1.183817291  1.285154406  0.271835930
## [379,] -0.100434292 -0.148112235  0.886936726  0.259148546  0.704812541
##                 PC6
##   [1,]  0.116709537
##   [2,]  0.110173000
##   [3,]  0.151011377
##   [4,] -0.343807479
##   [5,] -0.068417317
##   [6,] -0.420280958
##   [7,]  0.014839886
##   [8,]  0.336718257
##   [9,] -0.045952454
##  [10,]  1.939826284
##  [11,] -0.146897222
##  [12,]  0.183314250
##  [13,]  0.114162471
##  [14,] -0.102727402
##  [15,]  0.196911289
##  [16,] -0.296960713
##  [17,] -0.346683316
##  [18,]  0.385229903
##  [19,]  0.250212417
##  [20,]  0.210997273
##  [21,]  0.178758339
##  [22,] -0.003801151
##  [23,]  0.217319459
##  [24,] -0.187966712
##  [25,] -0.249408299
##  [26,]  0.582504343
##  [27,] -0.264956027
##  [28,] -0.324073726
##  [29,]  0.392690074
##  [30,]  0.433561922
##  [31,] -0.044052794
##  [32,] -0.172924722
##  [33,] -0.273046392
##  [34,] -0.339264995
##  [35,]  0.377235819
##  [36,] -0.090271827
##  [37,]  0.414287669
##  [38,] -0.393701821
##  [39,]  0.033505637
##  [40,]  0.354862667
##  [41,]  0.077217544
##  [42,] -0.251343699
##  [43,]  0.437209594
##  [44,]  0.418033744
##  [45,]  0.092143326
##  [46,]  0.453442755
##  [47,]  0.025217332
##  [48,] -0.198309910
##  [49,]  0.187074835
##  [50,]  0.063584865
##  [51,]  0.411945392
##  [52,]  0.347020693
##  [53,] -1.602200768
##  [54,] -0.297652746
##  [55,]  0.140534670
##  [56,] -0.120117267
##  [57,]  0.295188323
##  [58,] -0.436240290
##  [59,] -0.241532009
##  [60,] -0.152644965
##  [61,] -0.340782009
##  [62,] -0.237639469
##  [63,]  0.300926071
##  [64,] -0.253457399
##  [65,] -0.123036265
##  [66,] -0.318934216
##  [67,]  0.157579795
##  [68,] -0.260813996
##  [69,] -0.245354609
##  [70,] -0.305254302
##  [71,] -1.882250425
##  [72,]  0.409598000
##  [73,]  0.232202465
##  [74,] -0.149057573
##  [75,]  0.545903188
##  [76,]  0.277588617
##  [77,]  0.361912198
##  [78,] -0.478016137
##  [79,] -0.412381253
##  [80,] -0.183130748
##  [81,]  0.233456245
##  [82,] -0.356154388
##  [83,]  0.449569521
##  [84,] -0.185788498
##  [85,] -0.219609958
##  [86,] -0.001711114
##  [87,] -1.559617792
##  [88,] -0.428893296
##  [89,] -0.349853393
##  [90,]  0.067731920
##  [91,]  0.142796842
##  [92,] -0.180830638
##  [93,]  0.315292384
##  [94,]  0.557663845
##  [95,] -0.172373827
##  [96,]  0.407727459
##  [97,]  0.327538602
##  [98,]  0.346056104
##  [99,]  2.163269668
## [100,]  0.345529449
## [101,]  0.138719045
## [102,] -0.279523523
## [103,] -0.084975054
## [104,]  0.337408982
## [105,]  0.436700603
## [106,]  0.388716289
## [107,]  0.023800405
## [108,] -0.344894615
## [109,]  0.380430817
## [110,]  0.059212100
## [111,] -0.160062648
## [112,]  0.451808896
## [113,] -0.328134576
## [114,] -0.232509061
## [115,]  0.417691744
## [116,] -0.283499777
## [117,] -0.334241319
## [118,] -0.354492127
## [119,]  0.016626218
## [120,]  0.329368287
## [121,]  0.014802916
## [122,]  1.788209994
## [123,] -0.225290106
## [124,] -0.049381001
## [125,] -0.176037238
## [126,] -0.147416810
## [127,]  0.274931744
## [128,] -0.288402296
## [129,] -0.238830171
## [130,] -0.321394130
## [131,] -0.060804904
## [132,] -0.198430755
## [133,] -0.201882037
## [134,] -0.416230299
## [135,] -0.104823016
## [136,] -0.259292999
## [137,]  0.309515655
## [138,]  0.473433423
## [139,] -0.224455247
## [140,] -0.113549634
## [141,] -0.029270791
## [142,] -0.408139727
## [143,] -0.249679273
## [144,]  0.052432954
## [145,]  0.123609326
## [146,]  0.110721474
## [147,]  0.039482206
## [148,] -0.055563924
## [149,] -0.301541438
## [150,]  0.339761189
## [151,] -0.143565175
## [152,]  0.495882321
## [153,] -0.338275303
## [154,] -0.259013852
## [155,] -0.268105530
## [156,] -0.980893416
## [157,] -0.246803124
## [158,] -0.078306763
## [159,]  0.382030122
## [160,]  0.087323777
## [161,]  0.376505108
## [162,]  0.053401289
## [163,] -0.338300621
## [164,] -0.183747770
## [165,]  0.432642111
## [166,]  0.187719391
## [167,] -0.323645603
## [168,]  0.829006715
## [169,]  0.043491740
## [170,] -0.248046133
## [171,] -0.060255793
## [172,] -0.083545793
## [173,] -0.167508321
## [174,] -0.089468938
## [175,] -0.143831223
## [176,]  0.323860642
## [177,] -0.174432941
## [178,] -0.239734115
## [179,]  0.497289814
## [180,] -0.327540210
## [181,] -0.151688764
## [182,]  0.197182238
## [183,] -0.042715485
## [184,]  0.044010655
## [185,] -0.925270972
## [186,]  0.322942444
## [187,] -0.036587651
## [188,]  0.356359819
## [189,]  0.423139332
## [190,] -0.257850948
## [191,]  0.463686146
## [192,] -0.032295644
## [193,] -0.221120598
## [194,]  0.347410914
## [195,] -0.102882758
## [196,] -0.052886406
## [197,]  0.099771649
## [198,]  0.161046943
## [199,]  0.245795874
## [200,]  0.272924190
## [201,]  0.339839246
## [202,]  0.395294558
## [203,] -0.065386536
## [204,]  0.561844444
## [205,] -0.271407182
## [206,] -0.059059407
## [207,]  0.083045883
## [208,]  0.377344777
## [209,]  0.334594979
## [210,]  2.210117773
## [211,] -0.225352991
## [212,]  0.659498155
## [213,]  0.005821771
## [214,] -0.246898562
## [215,]  0.168733702
## [216,] -0.366893261
## [217,] -0.293117425
## [218,]  0.423293245
## [219,] -0.277523269
## [220,]  0.108760866
## [221,]  0.070710680
## [222,]  0.163384108
## [223,] -0.232906221
## [224,]  0.408184032
## [225,] -0.300209061
## [226,] -0.343281023
## [227,]  0.380266460
## [228,]  0.475769439
## [229,] -0.240418547
## [230,]  0.118544474
## [231,]  0.411577815
## [232,] -0.017746096
## [233,] -0.022662183
## [234,] -0.215224961
## [235,] -0.336453644
## [236,] -0.208327609
## [237,]  0.415886191
## [238,]  0.260849310
## [239,] -0.336942900
## [240,] -0.122484819
## [241,] -0.025660118
## [242,]  0.330693931
## [243,]  0.187450418
## [244,]  0.092254142
## [245,] -0.103389100
## [246,] -0.135338511
## [247,] -0.081072198
## [248,]  0.345962874
## [249,] -0.250967381
## [250,] -0.344899324
## [251,] -0.429960219
## [252,] -0.282830186
## [253,]  0.174435063
## [254,] -0.002994835
## [255,] -1.217412358
## [256,]  0.360421127
## [257,] -0.146287428
## [258,] -0.133025274
## [259,] -0.126146676
## [260,]  0.220778323
## [261,]  0.108029807
## [262,]  0.349752615
## [263,]  0.200005121
## [264,] -0.101933578
## [265,] -0.161334026
## [266,]  0.285586865
## [267,] -0.238563544
## [268,]  0.083679922
## [269,]  0.509906873
## [270,] -0.146139621
## [271,]  0.334416111
## [272,]  0.473647831
## [273,]  0.136442835
## [274,] -0.251405937
## [275,]  0.114366181
## [276,]  0.048022334
## [277,] -1.054946234
## [278,] -0.700681151
## [279,] -0.434292485
## [280,]  0.255500421
## [281,] -0.124820953
## [282,] -0.258508925
## [283,]  0.519297048
## [284,]  0.418680932
## [285,] -0.218443452
## [286,] -0.216123751
## [287,]  0.115923969
## [288,] -0.027866918
## [289,] -0.058716464
## [290,] -2.000384525
## [291,]  0.277974900
## [292,] -0.293421787
## [293,] -0.259635342
## [294,]  0.059625913
## [295,]  0.971487465
## [296,] -0.150615259
## [297,] -0.400937784
## [298,]  0.238954410
## [299,] -0.144937084
## [300,]  0.201952185
## [301,] -0.447834040
## [302,]  0.281901496
## [303,] -0.203869133
## [304,] -0.134202490
## [305,] -0.059036104
## [306,] -1.689975498
## [307,]  0.458648969
## [308,]  0.521154125
## [309,]  0.178933466
## [310,]  0.097184547
## [311,]  0.178727506
## [312,] -0.114849810
## [313,] -0.177928676
## [314,]  0.278091472
## [315,] -0.424718686
## [316,]  0.421376781
## [317,] -0.381796482
## [318,] -0.221941061
## [319,] -0.754255469
## [320,]  0.249838558
## [321,] -0.111526776
## [322,] -0.207650126
## [323,] -0.362767449
## [324,]  0.207891984
## [325,]  0.340268457
## [326,]  0.368766457
## [327,]  0.012058601
## [328,] -0.149559490
## [329,]  1.463155184
## [330,]  0.382942476
## [331,] -0.032112095
## [332,]  0.397084457
## [333,] -0.354911460
## [334,] -0.233823936
## [335,]  0.146812456
## [336,] -0.250028422
## [337,]  0.205107833
## [338,] -0.667916271
## [339,] -0.159417162
## [340,]  0.044940196
## [341,]  0.444365443
## [342,]  0.218371896
## [343,] -0.083864131
## [344,] -0.066718642
## [345,]  0.460637350
## [346,]  0.010040209
## [347,] -0.249703684
## [348,]  0.069849151
## [349,]  0.133553509
## [350,] -0.337335972
## [351,]  0.358285729
## [352,]  0.221064477
## [353,] -0.125296735
## [354,] -0.070458295
## [355,] -0.224997131
## [356,]  0.501370980
## [357,] -0.349367892
## [358,]  0.380452253
## [359,] -0.271394600
## [360,] -0.258419685
## [361,]  0.402658885
## [362,] -0.468027915
## [363,] -0.324990632
## [364,]  0.142034987
## [365,] -0.347928412
## [366,] -0.351391164
## [367,] -0.285977778
## [368,] -0.971457197
## [369,] -0.181523245
## [370,] -0.240725882
## [371,]  0.387573331
## [372,] -0.229079837
## [373,] -0.209054420
## [374,]  0.036780440
## [375,]  0.503922523
## [376,] -0.173505314
## [377,] -0.787406645
## [378,]  0.319960047
## [379,]  0.154968029
# Identifying the scores by their survival status
sparrtyp_pca <- cbind(data.frame(Cancer$Survivor),Cancer_pca$x)
sparrtyp_pca
##     Cancer.Survivor          PC1          PC2          PC3          PC4
## 1             Alive -1.493744354  1.672703734 -0.797771118 -0.639380539
## 2             Alive  0.426322428 -0.124086338 -0.222112841  0.478038848
## 3             Alive  1.694207768 -0.545124348  0.069937198 -1.032701826
## 4             Alive -1.767583528 -0.885302494 -0.030847119 -0.208720400
## 5             Alive  0.043714825 -1.603388200 -0.903121553  0.849669634
## 6             Alive -1.028534021  0.502739380  0.863904840  0.421284750
## 7             Alive -1.338771984  0.023023987 -0.740136022  1.021953281
## 8              Dead  0.406514411 -0.944219552 -1.935001240  2.169992691
## 9             Alive  4.993025728 -0.305103355  0.801778453  0.176933443
## 10            Alive  1.937948477  0.689507346  0.639790414 -2.348269489
## 11             Dead -1.756901401  0.140915113 -1.036789014 -0.816405788
## 12            Alive  1.296312778 -1.473829054  1.127778467 -0.112920985
## 13            Alive -0.090142691 -0.016296775 -1.070302648 -0.891412586
## 14            Alive -0.076244034  1.581531699 -0.943407970  1.540387096
## 15            Alive  1.004107956  1.120512340 -0.515080564 -0.672554789
## 16            Alive -1.005634503  0.998331229 -1.092830786  0.057925043
## 17            Alive -0.538374841 -1.839056096  0.934166263 -0.882076640
## 18            Alive  0.204445317  0.244548369  0.249012257  1.256474649
## 19            Alive -0.419443766 -0.379535399  1.728764442  0.083365143
## 20            Alive -0.252782392  0.344103196  0.155613436 -0.655869450
## 21            Alive -0.036353656 -0.349284099  0.645811404  0.425442619
## 22            Alive  0.504291512  0.121502823 -0.952996651 -0.061329141
## 23            Alive -0.618672209 -1.285043286 -0.036105811 -0.229784303
## 24            Alive  1.459334722 -1.104003050  1.630015919 -0.538883137
## 25            Alive  0.693501261  3.217631237  1.088615995 -0.680914229
## 26            Alive  1.342457422  2.945510521  0.104659090 -0.694326558
## 27            Alive  2.475721782  2.107120006  1.821692902  0.042150966
## 28            Alive -1.137184838 -0.018509243  0.662500068  1.019754895
## 29            Alive -0.082096727  0.062026127 -0.404849247 -0.143815038
## 30            Alive -0.951459346 -0.397603334  0.033425845 -1.324785280
## 31            Alive  0.004306142 -1.599200390 -0.821234717  0.828802331
## 32            Alive -1.358590305 -0.557530387 -1.182191573  0.826013095
## 33            Alive -1.790419403 -0.472260893  0.282426323 -0.357402908
## 34            Alive -0.908445651  0.994824271 -0.546660828 -0.042005466
## 35            Alive  1.245709794  0.857794242 -1.178327309  1.397760831
## 36            Alive -1.439873416 -0.186081367  0.144133667  0.662537801
## 37            Alive  0.636390371  0.900377415 -1.197745317  0.553485818
## 38            Alive -1.304428696  0.097530771  1.328492259  0.221100925
## 39            Alive -0.097417933 -0.858136005  0.513336501  0.257353363
## 40            Alive -0.188925650 -0.025716107  1.521237025 -0.147451873
## 41             Dead  2.535953943 -0.283072938 -1.273811462 -0.496124138
## 42            Alive -1.364589888  0.380987232 -0.926166470 -0.409214549
## 43            Alive -1.095258604 -1.245692755 -0.025636708 -0.959504567
## 44            Alive  0.018958421  0.185171532  0.594724325 -0.026225609
## 45            Alive -1.483766860  0.205593899 -0.521531513  0.532329976
## 46            Alive  0.803570710 -0.823728790  0.269737583 -1.940110944
## 47             Dead -0.776759752  0.318065419 -0.898736044  2.118307298
## 48            Alive -1.440160549  0.277491231 -0.933452622 -0.172656258
## 49            Alive  0.550199236  0.443259288  0.544534206 -0.061726221
## 50            Alive -1.959716237  0.269905907 -0.358261698 -1.104900464
## 51            Alive  0.283946083 -0.215989222  0.718462913  1.705505213
## 52            Alive  0.584420507 -1.170636855 -0.658910102 -2.000608348
## 53            Alive  2.164109035 -2.375151885  0.202704168 -1.926001263
## 54            Alive  1.673683848 -0.438611018 -0.189966395 -1.566014043
## 55            Alive -1.630123732  0.631351549 -0.019980046  0.212113815
## 56            Alive -1.450559221  0.201501035 -0.069005014  0.333630589
## 57            Alive -0.534036352  0.291756051  0.624478817 -1.023860005
## 58            Alive -0.354843129  3.274197111  2.410035980  0.361353654
## 59            Alive -1.178588655  0.226034827  0.171909908  0.786762124
## 60            Alive -1.248535425  0.638963394  0.202025885  0.279803670
## 61            Alive -0.944827480  1.241989527  0.467351263  0.104831170
## 62            Alive -1.056029210  0.031887224 -0.922233051  1.020017722
## 63            Alive -0.473763736 -1.839525046  0.381440310  1.043813308
## 64            Alive  1.681009012 -0.528168820  0.166784745 -1.236306623
## 65             Dead -1.312786276  0.965097163 -0.969708882 -0.635102168
## 66            Alive -1.639877002 -0.931529988  1.401477586  0.658502060
## 67             Dead  4.455166578  1.087532562  0.124772958  2.053348449
## 68            Alive -0.707613499  0.590986037  1.179291019  1.595111891
## 69            Alive -1.710632794 -0.549715482 -0.153074842 -0.100695874
## 70            Alive -1.171903123  0.100583865  0.469100757  0.412780064
## 71            Alive  3.302612150 -1.737283578  1.502810946 -1.179097587
## 72             Dead  2.121655213  2.644141124 -2.473204090 -0.044893038
## 73            Alive  0.528823585 -0.636078944  0.137430927  2.495082814
## 74            Alive -1.868775707  0.569029628  0.581800057 -1.084485611
## 75            Alive  0.683905846  1.767290796  0.241693051 -1.337566812
## 76            Alive  0.821006546 -1.188104492  0.917466077 -1.089980478
## 77            Alive -0.499967072 -0.063567628 -0.217092609 -1.242667319
## 78            Alive  0.056071716 -1.653376800  1.664161542  0.435774870
## 79            Alive  0.099588612 -1.161140621  0.358003056 -0.058098223
## 80            Alive -1.638985742  0.150875793 -1.403816856 -0.700686152
## 81            Alive  0.865297254  1.214733944  1.463461173 -0.297882350
## 82            Alive -1.545124764  0.127252910 -0.935729044 -0.793110208
## 83            Alive -0.757282603 -0.365269832 -0.559376514 -1.125365040
## 84            Alive -1.494668798 -0.862217669 -1.017557513  0.729371690
## 85            Alive -1.198962297  0.090483632 -0.244225721  0.803338834
## 86            Alive  1.053228198  0.023027292  0.260206980  0.703883631
## 87            Alive  2.839883593 -2.296312935  0.510353279 -0.693661524
## 88            Alive  1.506058603 -1.812772768  0.528733408 -0.767001468
## 89            Alive -1.539415867 -0.136768478  0.768955037 -0.049503375
## 90            Alive -2.166532837  0.071753733  0.343483494 -0.898166612
## 91             Dead  0.893002750 -1.772886261  0.734063638 -0.797845672
## 92            Alive -0.677904182 -0.104397875  0.169469929  2.673756815
## 93             Dead -0.646604416 -0.740495104  0.063231982 -1.095809541
## 94             Dead  1.683330979  1.567742424 -0.698706197  1.431672587
## 95            Alive -1.509921397  0.297490480  0.490010821 -0.323083740
## 96            Alive -0.135237286  0.293266912 -1.015571227 -0.225694168
## 97             Dead  0.027644129 -1.133291443 -1.997458759  1.032137750
## 98            Alive -0.637273583 -0.513850978 -0.306967375 -0.684532247
## 99             Dead  1.070049729 -2.036508976 -0.316339810 -0.094341352
## 100           Alive -0.455435814  0.089328755 -1.403983913 -1.027093674
## 101            Dead  4.600390311  2.244846920  0.532264308  1.259266636
## 102           Alive -0.787145836  1.086091949  0.549806202  1.093912587
## 103           Alive  0.655142324 -1.683984928 -2.308143986  2.208715115
## 104            Dead -0.428540034 -0.840500324 -1.048098702 -0.027665882
## 105           Alive -0.110654721 -0.123171275 -0.175937919  0.338031509
## 106           Alive -0.734249607 -1.236231879 -1.090037416 -0.386975718
## 107            Dead  0.296584193 -0.577728068 -2.014640498  0.588158511
## 108           Alive -1.410702952  0.429684625 -0.958296105 -0.866024725
## 109           Alive -0.418905210 -1.232525386  1.863199813  1.081316900
## 110           Alive  0.446752555  1.508585940 -0.342268303 -0.736468382
## 111           Alive -1.134059417  0.782686222 -0.521004605 -0.152263500
## 112            Dead  1.181466882 -2.299898160  0.735344703  0.997333267
## 113           Alive  1.830654533  1.883074076  0.954309940  0.626252247
## 114           Alive  0.454774207 -0.643039459  0.237045213  0.759165544
## 115           Alive  0.864920996 -1.531113286  1.149483739 -0.984234084
## 116           Alive -0.897625868  0.218458064 -0.870977930  0.772271080
## 117           Alive  1.357865125 -1.941049776  0.946671254 -0.674767960
## 118           Alive -0.915336154  1.327339693  0.352068802 -1.370754921
## 119           Alive  0.094948933 -0.356826249  1.052712045  0.237447671
## 120           Alive -0.037442692 -0.108870167 -0.518461408  0.323952099
## 121           Alive -0.703244230 -0.760629115  0.236405707 -1.666145723
## 122           Alive  1.727474232 -1.256161661  0.911292089  0.280268540
## 123           Alive  1.839479021  0.845697621 -0.141543565  0.392072998
## 124           Alive  0.275373090  0.726740366  0.643511448 -0.752337791
## 125           Alive -0.732974709  1.225314046 -0.703247765  0.876777966
## 126            Dead -0.921856464  0.796384898 -2.658215899  0.486234753
## 127           Alive -0.151799435 -0.761905068  1.710990722  1.051731292
## 128           Alive -1.471716143 -0.654343538 -1.425218658  0.191711126
## 129           Alive -1.483838817 -0.227422742  0.005677556  0.103891666
## 130           Alive -0.899242135  0.043994478  0.476955011  1.186170494
## 131           Alive -1.358439633  0.497908624 -1.167958845  0.193782726
## 132           Alive  0.549771469 -0.569819028  0.116818203  0.221134190
## 133           Alive -1.825714544 -0.294808189  0.619015786 -0.318205481
## 134           Alive -1.466418848 -0.825197537  0.473859265  0.509772598
## 135            Dead  0.713759778 -0.436347722 -1.423945946  0.210208666
## 136            Dead  0.095641779  1.526711941  0.249630093  2.345493852
## 137           Alive -0.311491252 -0.719233132  0.764263980  0.606336637
## 138            Dead -0.482193479  0.590787139 -0.436621861 -0.920884510
## 139            Dead  1.024336162  0.440548826 -0.998470261 -0.555076086
## 140           Alive  2.074951928 -0.323134611  1.585536035 -0.925846944
## 141           Alive -1.891283328 -0.671701731  0.262065322  0.249157996
## 142           Alive -0.768896963 -0.184566117  1.838693762  1.680165112
## 143           Alive -0.660225602  1.111821771 -0.488335117  1.229777710
## 144            Dead  0.458314079  0.872057326 -1.262688367 -0.394557457
## 145            Dead  0.202499186  0.236773800 -0.635093302  0.249780704
## 146           Alive -0.635694229 -0.225009929  1.204353392 -1.218165045
## 147           Alive -1.314850127  0.558262177  1.185628313  0.999319862
## 148            Dead  2.618727317 -1.043294960 -0.131770830  1.161272958
## 149           Alive -1.867933212 -0.735989177 -0.971686550 -0.761863164
## 150           Alive -0.390204192 -0.137821477  0.220960666 -0.609509106
## 151           Alive -1.169108179  0.192370763  1.849895119  1.591382674
## 152           Alive -0.593384345  0.170296655 -0.789961437 -1.081723093
## 153            Dead -1.153893444  0.470099262 -0.943547532  0.043877107
## 154           Alive -1.299586961  0.646325766  0.756131408 -0.633505535
## 155           Alive -1.312753509  0.646956638 -1.191403488 -0.628395922
## 156           Alive  2.158951805 -0.669181055  0.329330268 -2.652868558
## 157           Alive -0.888545794  0.212970263 -0.609333802  1.384522112
## 158           Alive -1.604599290 -0.895420185  1.536550848  1.466041850
## 159           Alive -0.695240701 -1.437349712 -0.294419793  0.105308219
## 160            Dead  1.698058938  0.861942358 -2.379230129  0.682957573
## 161           Alive  0.523091631  0.622823965 -2.532738018  0.414152379
## 162           Alive -1.639464234 -0.668476601 -1.067754195  0.831399161
## 163           Alive -1.775434759 -0.854401433 -0.150230446 -0.275686146
## 164           Alive -1.300191877  0.924773079  0.692943522 -0.083020548
## 165           Alive  0.127243391  0.547570383 -0.822898988 -0.399221133
## 166           Alive  0.728909729 -1.777883731 -1.474530685 -1.729305188
## 167           Alive -0.691130861  0.504125474 -0.083355531  0.385479113
## 168           Alive  4.057107584  0.177251126  2.338537102  0.287960419
## 169           Alive  0.065928057 -1.066260062 -0.766093466  0.786318654
## 170           Alive -1.537449988  0.126535183  1.129984140  0.112397316
## 171            Dead  0.005212931  0.571207430 -0.800002711 -1.395337324
## 172           Alive  1.307010016 -1.130265555 -0.298412422 -1.569287554
## 173           Alive -1.400091197 -0.281929928  0.503682489  0.734624858
## 174           Alive -1.914378275 -0.015175249  0.090929135 -0.639031301
## 175           Alive -1.354059138  1.369758171  0.970119313 -0.448346287
## 176           Alive  1.278137221 -1.653045958  0.582176145  0.663913439
## 177            Dead -0.240072950  1.468050171 -1.146791696  0.313983803
## 178           Alive -1.192542565 -0.620681157  0.393013804  1.386142742
## 179           Alive  1.517499402  2.446494185 -0.097915083  0.552779780
## 180            Dead  0.419667049 -0.327707583 -0.647757875 -0.752472503
## 181           Alive -1.183491054  2.047841110  1.056237863 -0.386605606
## 182            Dead -0.049231716  0.736575008  0.077583188 -0.705296875
## 183            Dead -1.497163756 -0.391927377 -2.671606811  0.257351508
## 184           Alive  1.362728567  0.566668154 -0.177208297  0.688607859
## 185           Alive  3.022520941 -0.826120544  0.734638502 -0.813207184
## 186           Alive -0.646848816  0.019961075  0.140097904 -1.345604301
## 187           Alive  0.841699831 -1.772549530 -0.373832896 -2.173967292
## 188           Alive -0.341629561 -0.113562351 -0.165011337 -0.351171147
## 189            Dead  0.597265999  2.425823378  1.007898127 -0.923443496
## 190           Alive -1.161264597  0.015537197  0.541717900  1.081599330
## 191           Alive -0.477014120 -0.313853416 -0.666580443 -0.171072190
## 192           Alive -2.115125949 -0.729760082  0.102680575 -0.379831150
## 193           Alive -0.991130507  1.160119732 -0.454562005 -0.255797516
## 194           Alive -0.707735717 -1.202340369  0.313311997 -0.079193489
## 195           Alive  3.115036491 -0.278203347 -0.068038843  0.730365425
## 196           Alive -1.696392904 -0.279442921 -1.520016658 -0.119474656
## 197           Alive  0.151090645 -0.052353299 -0.654184084  0.093232715
## 198           Alive  1.330786502 -1.333832490  1.198984292 -0.592071242
## 199           Alive  0.296675856  0.507260694 -0.459773048  0.471858283
## 200           Alive -0.422623151 -0.772830338  1.475442657  0.229622630
## 201           Alive -0.318075869 -0.206265532  0.193138644 -0.150273909
## 202           Alive -0.085308348  0.324848824 -0.506897761 -0.413457726
## 203            Dead -1.822877611 -0.578840959 -1.943795566 -0.354374768
## 204            Dead  1.201683038  1.016703999 -1.617844139  1.145915109
## 205           Alive -1.807181645 -0.673704761 -0.909165251 -0.542600144
## 206           Alive -1.784093888 -0.101950630 -1.523967142 -0.547484916
## 207           Alive -0.078106596  0.540840034  0.980990841 -0.492489469
## 208           Alive -0.721328123  0.145142743  1.245670834 -1.005611527
## 209           Alive -0.483839459 -0.454229646  0.058240719 -0.240884895
## 210           Alive  0.663630444 -2.030515942  1.095559877 -0.315653418
## 211           Alive  1.978468906 -1.541564858  0.344229726  0.254916972
## 212            Dead  2.937647970  0.023153745 -1.467099553  2.004769891
## 213           Alive -0.086636710  1.891839624  1.573096232  0.223299508
## 214           Alive -1.481813930  0.006331169 -1.173928063 -0.250137785
## 215           Alive  0.623006822 -0.037759847 -0.710766534  0.184537311
## 216            Dead  1.991882118 -1.666919941 -2.805934883 -0.871488718
## 217            Dead  0.744165906 -0.860059687 -1.328696095  1.365529752
## 218           Alive  0.641119818 -0.445632455  0.162013092 -2.055341520
## 219           Alive -1.586401627 -0.388025617 -1.097489991 -0.453696582
## 220            Dead  4.773395918  2.278577670 -1.336404778  0.510730406
## 221            Dead  2.921320323 -0.012042086 -1.874368061 -0.045263697
## 222            Dead  0.503935335  1.035837075 -1.154051231 -0.866417161
## 223           Alive -1.241990069  0.411074638  1.790709487  0.707551103
## 224           Alive -0.133856941 -0.846749537  0.481837944  1.031203316
## 225           Alive -1.486223026 -1.226757723  0.663500601  1.212738370
## 226           Alive -0.762041381  1.164340422  1.896521625  1.074683686
## 227           Alive  2.005021660  0.341436716 -0.409217808 -0.832010193
## 228           Alive  1.814305601  1.684900471  0.545885187 -0.444700098
## 229           Alive -1.411373860 -0.029800132 -1.219717248 -0.012627251
## 230           Alive -0.324175998  0.181346052  0.453617491 -1.500433205
## 231           Alive -0.456860329  0.176546846  0.852740264 -0.298237857
## 232           Alive -1.210396528  0.443593233 -1.157566359 -0.418875718
## 233           Alive  0.367888943  1.034558583 -0.899804344 -1.320083756
## 234           Alive -1.737267642 -0.768492804 -0.717586622 -0.042347936
## 235           Alive -1.509987525  0.519084836  0.532663661 -0.793096619
## 236           Alive -1.290446225  1.701929130 -0.262965485 -0.898972118
## 237           Alive  3.655612544  1.679581237 -0.078271387  0.366568656
## 238           Alive  0.611276361 -1.193837776  1.025840807 -1.693775105
## 239            Dead  6.711875034  1.215508748 -1.279625142  0.587766000
## 240           Alive -1.281390399 -0.456797389  0.383696463  1.327109609
## 241            Dead  0.776720455  0.873249312 -0.255587193  0.950034593
## 242           Alive  0.008347450  1.173046306  1.625650682 -0.126758712
## 243           Alive -0.958826089 -0.492058288  0.745646701 -1.985299776
## 244           Alive  1.609087788  0.768291741  1.106856868  1.288165361
## 245           Alive  0.543831815 -0.344117364  1.084227436  0.743018250
## 246           Alive -1.795501728  0.797766300  0.941073658 -0.948765046
## 247           Alive -2.078996209  0.034041364  0.343126833 -1.053156920
## 248            Dead  0.486998129  0.122844418 -0.822868404  1.350720580
## 249           Alive -0.821657492 -0.011924402  0.873543779  1.971662603
## 250           Alive -1.398504155 -0.243599402  0.837410828  0.477686433
## 251           Alive  0.526594325 -1.361027292  1.730491888  0.644317870
## 252           Alive  0.120809384 -1.392425032 -0.882175385  0.251835439
## 253           Alive -0.289560811 -1.753881720  0.731478923  1.008115634
## 254           Alive  2.350354264 -1.374432502  0.783487702  1.516771930
## 255           Alive  2.529945185 -0.796264796 -1.084229732 -1.768591624
## 256           Alive -0.594294620  0.606268901  0.546284310 -1.512570945
## 257           Alive -1.406577585  0.312852106 -0.020482861  0.091002001
## 258           Alive -1.651971076 -0.143369845 -1.143133022 -0.250064542
## 259           Alive  0.415871178 -0.214174686  0.915948123  0.956618386
## 260           Alive -0.286827613 -0.440600376 -0.511227621 -0.188717119
## 261           Alive -0.645411407  0.058506107 -2.305257330  2.581332331
## 262           Alive -0.628353063 -1.040695063  1.499765220  0.328717274
## 263           Alive -0.136446586 -0.912547265  0.240795333  0.609862680
## 264            Dead -1.777655604 -0.274014123 -1.028075306 -0.764011769
## 265           Alive -1.357302997  2.288698502  1.019344070 -1.133889152
## 266           Alive -1.150407815 -1.178196185  0.453312973 -1.488628969
## 267           Alive -0.854919366  2.319121839 -0.534036982 -0.401249649
## 268           Alive  1.748954057 -2.489466264  0.147763981  1.527744484
## 269            Dead -0.738423976 -0.871268532 -1.716222096 -0.549433967
## 270           Alive -0.346935263  1.923554748 -1.292856361 -0.360145431
## 271            Dead  2.611945346 -0.868543943 -0.456914061  1.833405222
## 272           Alive -0.054669716  0.467014101 -0.459580646  0.187565076
## 273           Alive  0.590763284  0.081986670 -0.821826225  1.066920091
## 274           Alive -0.771766282  0.497567733 -0.144543170 -0.043136586
## 275           Alive  0.287407340 -0.999343796 -0.141647094  1.726767706
## 276           Alive -1.904210848 -0.711924915 -0.636156799  0.229311959
## 277           Alive  1.980934953 -2.144737237 -1.558960290 -1.734660915
## 278            Dead  4.349982486  0.818990696 -1.850629065  0.156456507
## 279           Alive -1.601460087  0.466219801  0.555412046 -1.282120597
## 280           Alive  1.110817200 -0.894199685  0.626718163 -1.090577512
## 281           Alive -1.635586546  0.585764692  0.351472824 -0.436299965
## 282           Alive -0.910449829 -0.063109780 -0.243265787  1.440217859
## 283            Dead  0.979721615  0.904442368 -1.232199254  1.008144535
## 284           Alive -0.472435837 -0.521473629  0.942802823  0.140237047
## 285           Alive  0.298128461 -0.439838094 -0.230211394  0.045875504
## 286            Dead  0.876478490 -0.632485240 -2.150246922  0.523252544
## 287           Alive  0.030556752 -0.246001099 -1.050954176 -0.130320899
## 288           Alive  0.489276289  0.149716001  1.343990756 -0.776952747
## 289           Alive  1.167193218  4.324487587  0.744165112 -1.104452819
## 290            Dead  5.639123713  1.493129585  0.436631086  0.391589194
## 291           Alive  0.076038156  2.149080398  1.231684279 -0.889701456
## 292           Alive -1.306362503  0.777428880 -0.836033189 -0.505010722
## 293            Dead -1.492629535  0.346667458 -1.594060891 -0.744201427
## 294           Alive  0.548191410  0.159332266  1.521957843  0.691090269
## 295           Alive  3.173294742 -0.713640891  1.483201289 -0.597042450
## 296           Alive -1.711510331  0.207909220 -0.931632873 -0.732023246
## 297           Alive -1.420928885 -1.297938310  0.314667960  1.070874265
## 298           Alive -0.397038374 -0.140558009 -0.100049951 -1.210608408
## 299           Alive -1.338159554  0.850035604  0.991498508  0.275292019
## 300           Alive  1.238726422 -0.682019739 -1.206227105 -1.584533216
## 301           Alive  0.476798036 -0.538294379  1.306977504  0.589987890
## 302           Alive  0.451358041  0.509847268 -0.404959275  1.025191596
## 303           Alive -0.410664267  1.809811675  0.163254213  1.203959868
## 304           Alive  0.631511135  4.553878477  0.617849698 -0.258625983
## 305           Alive  0.606275351  1.307303704 -1.190130416 -1.085147986
## 306            Dead  3.760469200 -1.318016453 -1.571659239 -0.958198521
## 307           Alive  0.283257978  0.334225557  0.900109850  1.387190281
## 308           Alive  1.205872572 -1.025116718 -0.694241491 -0.489820821
## 309           Alive -0.547890175 -1.378267017  0.199506501  0.006777245
## 310           Alive  0.675442079 -0.040092847  0.040280714  1.538300103
## 311           Alive -0.347420655 -1.297275709 -0.084885546  0.216594996
## 312           Alive -1.082694803  1.058501944 -1.274637266 -0.535652316
## 313           Alive -0.809911038  0.678119879 -0.193503870  0.489931605
## 314            Dead  2.814192996  1.465015414  1.296910650 -1.024401483
## 315           Alive -1.219216145 -0.216402526  0.775638956  0.706433637
## 316           Alive -0.839858529 -1.160921154 -0.067522123 -0.376613864
## 317           Alive  1.906604890 -1.476681383 -0.028831221  0.037013607
## 318           Alive -1.128786006  0.395890021  0.040446729  0.390323605
## 319           Alive  4.980287452  1.400993226  0.386980437  0.646687478
## 320           Alive -0.396555408 -0.215395452 -1.222389233 -0.813225124
## 321           Alive -1.686147468  0.664222126  1.210799613 -0.375476795
## 322           Alive -0.771587552  0.001912498 -0.021523533  2.182231316
## 323           Alive  2.121003409 -2.080663494  0.161998088  0.897550000
## 324           Alive  0.183525269  0.711131176  0.676974276 -0.837925098
## 325           Alive -0.388480855 -0.019183155 -0.034180507 -0.379134234
## 326           Alive -0.270374270  0.372642009  0.619830911 -1.148519958
## 327           Alive -0.016309255 -0.272150173  1.123754077 -0.347941297
## 328           Alive -1.509365115 -1.227221931  0.110956778  1.437386493
## 329           Alive  1.128006246 -1.746278013  0.499382396 -1.619420542
## 330           Alive -0.013678857  0.097843119  0.408072714 -0.795855347
## 331           Alive  0.134239505  0.261168839  1.687827776  0.217195174
## 332            Dead  0.543266130  0.289044087 -1.889627887  1.415180585
## 333           Alive -1.694510184 -0.384164773  0.978956440 -0.619188118
## 334           Alive -1.177192240  0.755347480 -0.072837954  0.262273753
## 335           Alive -0.154704801 -0.482019591 -0.130393501  0.108703255
## 336           Alive -1.222393212 -0.140605864  0.470903440  0.854635087
## 337           Alive  0.985284375 -2.085350193 -0.309169317 -0.356636930
## 338           Alive  1.845084419 -1.284127961 -0.428328294 -1.460289251
## 339           Alive -1.537001279  1.111570387  0.652894920 -1.060718845
## 340           Alive  0.486580696 -0.438599188 -0.143918334  0.966749788
## 341           Alive -0.381846642 -0.365594889  0.626052636  0.039508221
## 342           Alive -1.058469609  1.839970213 -0.254329772 -0.731552164
## 343           Alive  1.953784231 -1.229071105  0.160259672  0.867246394
## 344           Alive -1.632770525 -0.310017947  0.586575867  0.624972262
## 345           Alive -0.069211481  1.179578849 -0.019456868 -1.025693279
## 346           Alive  0.924645953  0.318200997 -0.038558980 -0.176342543
## 347           Alive -1.679627649 -0.870249748  1.201962925  0.638583744
## 348           Alive -0.138978457 -0.327879510  1.445999742  0.018109114
## 349           Alive -0.306354427  2.443421548  0.256738595  0.723881262
## 350           Alive -1.082397105  0.511694553  0.396630701  0.376171916
## 351           Alive  1.560087096 -0.172608049  2.042673531  0.001387343
## 352           Alive  0.213890453  0.121650120 -0.363220480  0.143134581
## 353           Alive -1.243101129 -0.469575151 -1.404226113  1.148855158
## 354           Alive -1.723673624 -0.628891973  1.215101216  0.822337346
## 355           Alive -1.845736715 -1.246640827  1.218806001  0.592440275
## 356           Alive -0.533908899  0.509703545 -1.010222476 -1.067833304
## 357           Alive -0.621852817  1.060330174 -0.185420284  0.974853637
## 358            Dead -0.663822556 -0.698693563 -1.437208451 -1.000964685
## 359           Alive -1.464448793 -0.997923794  0.090438438  0.991886193
## 360           Alive -1.523194528  1.088366756 -0.015584201 -1.071387626
## 361           Alive -0.249284791 -0.495162923 -0.888175969  0.194375075
## 362           Alive -0.978278825  0.745196276  1.673492426  0.624652999
## 363            Dead  2.298810986 -0.090143085 -0.751106742 -0.561856912
## 364            Dead -0.641761160 -1.573225212  0.960424847 -0.179437036
## 365           Alive -1.237501132 -0.412442737  1.793811573  1.137104529
## 366           Alive -1.157403928  0.923508573 -0.442026074 -0.884941552
## 367           Alive -0.796933393  1.222876039  0.723404723 -0.237384378
## 368           Alive  2.646899548  0.301553970  0.690593527 -2.443750630
## 369           Alive -0.178975454 -0.138624086  1.105283992 -1.499072183
## 370            Dead -1.330874437  0.769296425 -0.127097036 -1.223980155
## 371           Alive  0.785519987  2.132318925  0.981263612 -0.639682484
## 372            Dead  4.528600634 -0.995996130  0.568209680 -0.292649916
## 373           Alive -2.215387412 -0.717213408  0.437807288 -1.098624561
## 374           Alive  0.852816653  0.697424945 -0.415247520  0.859928559
## 375           Alive  1.528575274  1.579100810  0.424898608  1.740887715
## 376           Alive  1.052831636  0.469776583  0.746395631 -0.477473960
## 377           Alive  3.308075529 -0.637217047 -0.361014725 -0.281269186
## 378           Alive  0.145308323 -0.337470348  1.183817291  1.285154406
## 379           Alive -0.100434292 -0.148112235  0.886936726  0.259148546
##              PC5          PC6
## 1    0.852277723  0.116709537
## 2   -0.014925567  0.110173000
## 3   -0.039058417  0.151011377
## 4   -0.771910136 -0.343807479
## 5   -0.078371793 -0.068417317
## 6    0.233248754 -0.420280958
## 7    0.038121315  0.014839886
## 8    0.548288673  0.336718257
## 9   -0.724303190 -0.045952454
## 10  -0.376692694  1.939826284
## 11  -0.204199065 -0.146897222
## 12   0.266696937  0.183314250
## 13   0.200775716  0.114162471
## 14   0.141353261 -0.102727402
## 15  -1.296448032  0.196911289
## 16   0.742413832 -0.296960713
## 17  -0.578346113 -0.346683316
## 18   1.134795943  0.385229903
## 19   0.402986436  0.250212417
## 20   0.860603335  0.210997273
## 21   0.372107468  0.178758339
## 22   0.135596833 -0.003801151
## 23  -0.280109421  0.217319459
## 24   1.064729564 -0.187966712
## 25  -2.330312186 -0.249408299
## 26  -0.785747318  0.582504343
## 27  -2.125689786 -0.264956027
## 28   0.143564512 -0.324073726
## 29   0.043817854  0.392690074
## 30   0.016907630  0.433561922
## 31  -0.096628489 -0.044052794
## 32  -0.330970546 -0.172924722
## 33  -0.542183270 -0.273046392
## 34   0.292432820 -0.339264995
## 35  -0.230660457  0.377235819
## 36  -0.393665514 -0.090271827
## 37   0.437914429  0.414287669
## 38  -0.155155562 -0.393701821
## 39   0.029439452  0.033505637
## 40  -0.286733286  0.354862667
## 41  -0.691155605  0.077217544
## 42  -0.084453563 -0.251343699
## 43  -0.544787256  0.437209594
## 44  -0.312285920  0.418033744
## 45  -0.202487124  0.092143326
## 46  -0.213877418  0.453442755
## 47   0.308120927  0.025217332
## 48   0.076695703 -0.198309910
## 49  -0.634281043  0.187074835
## 50  -0.742921582  0.063584865
## 51   0.429398197  0.411945392
## 52   0.454750957  0.347020693
## 53   0.605914036 -1.602200768
## 54   1.244480037 -0.297652746
## 55   0.215871580  0.140534670
## 56   0.063005452 -0.120117267
## 57   0.669994233  0.295188323
## 58   2.502769179 -0.436240290
## 59   0.247357475 -0.241532009
## 60   0.179044984 -0.152644965
## 61   0.693575290 -0.340782009
## 62   0.191600412 -0.237639469
## 63  -0.465299021  0.300926071
## 64   1.216190250 -0.253457399
## 65   0.024970627 -0.123036265
## 66  -0.668767345 -0.318934216
## 67  -1.489900944  0.157579795
## 68   0.263308423 -0.260813996
## 69  -0.540451474 -0.245354609
## 70  -0.339388614 -0.305254302
## 71  -0.118238924 -1.882250425
## 72  -1.314192531  0.409598000
## 73   0.843161685  0.232202465
## 74   0.002065102 -0.149057573
## 75  -1.608284497  0.545903188
## 76   0.637354405  0.277588617
## 77  -0.300754296  0.361912198
## 78  -0.079376450 -0.478016137
## 79   0.191212303 -0.412381253
## 80  -0.135813445 -0.183130748
## 81  -1.014695877  0.233456245
## 82  -0.096332740 -0.356154388
## 83  -0.112495907  0.449569521
## 84  -0.585327071 -0.185788498
## 85   0.150630291 -0.219609958
## 86  -1.086933498 -0.001711114
## 87   0.066738128 -1.559617792
## 88   0.643656650 -0.428893296
## 89  -0.188258747 -0.349853393
## 90  -0.445936393  0.067731920
## 91   0.341156668  0.142796842
## 92   0.405882517 -0.180830638
## 93  -0.767513218  0.315292384
## 94  -1.080548515  0.557663845
## 95  -0.437095352 -0.172373827
## 96   0.642455326  0.407727459
## 97  -0.070625404  0.327538602
## 98   0.140054208  0.346056104
## 99  -0.094161935  2.163269668
## 100  0.560281943  0.345529449
## 101 -1.010942778  0.138719045
## 102  0.984179992 -0.279523523
## 103  0.240582243 -0.084975054
## 104  0.077046929  0.337408982
## 105  0.196792323  0.436700603
## 106 -0.336972535  0.388716289
## 107  0.632602330  0.023800405
## 108 -0.101651534 -0.344894615
## 109 -0.304585111  0.380430817
## 110  1.406332814  0.059212100
## 111 -0.210024740 -0.160062648
## 112 -0.237945040  0.451808896
## 113  0.685943765 -0.328134576
## 114  0.470129822 -0.232509061
## 115 -0.541097522  0.417691744
## 116 -0.128040261 -0.283499777
## 117  0.499517827 -0.334241319
## 118 -1.073206670 -0.354492127
## 119  0.183785081  0.016626218
## 120  0.490323176  0.329368287
## 121 -0.328854978  0.014802916
## 122  0.754418800  1.788209994
## 123 -1.461521820 -0.225290106
## 124  0.616212060 -0.049381001
## 125  0.813571603 -0.176037238
## 126  0.662707828 -0.147416810
## 127  0.112226358  0.274931744
## 128 -0.481284081 -0.288402296
## 129 -0.469159558 -0.238830171
## 130 -0.191676482 -0.321394130
## 131  0.263406749 -0.060804904
## 132 -0.470229839 -0.198430755
## 133 -0.449230612 -0.201882037
## 134 -0.534711905 -0.416230299
## 135 -0.580685346 -0.104823016
## 136  0.760447203 -0.259292999
## 137  0.268751238  0.309515655
## 138  0.862037778  0.473433423
## 139 -0.681175727 -0.224455247
## 140 -0.179553069 -0.113549634
## 141 -0.686573604 -0.029270791
## 142 -0.464801156 -0.408139727
## 143  1.056964399 -0.249679273
## 144  1.037856081  0.052432954
## 145  1.069400578  0.123609326
## 146  0.311045179  0.110721474
## 147  0.144248090  0.039482206
## 148  0.005960761 -0.055563924
## 149 -0.777526175 -0.301541438
## 150  0.001859155  0.339761189
## 151  0.295730175 -0.143565175
## 152  0.289525424  0.495882321
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## 263 -0.011841605  0.200005121
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## 304  0.452803511 -0.134202490
## 305  0.839582865 -0.059036104
## 306 -0.168654341 -1.689975498
## 307  0.742119351  0.458648969
## 308  0.185091372  0.521154125
## 309 -0.282776412  0.178933466
## 310  0.724233244  0.097184547
## 311 -0.374740492  0.178727506
## 312 -0.301170989 -0.114849810
## 313 -0.567989774 -0.177928676
## 314 -0.754090861  0.278091472
## 315 -0.029531003 -0.424718686
## 316 -0.332337533  0.421376781
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## 318 -0.149885563 -0.221941061
## 319 -1.083846603 -0.754255469
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## 324 -0.201495035  0.207891984
## 325  0.583222451  0.340268457
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## 347 -0.657934688 -0.249703684
## 348  0.324021275  0.069849151
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## 355 -0.970712299 -0.224997131
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## 357  0.788314716 -0.349367892
## 358 -0.267520648  0.380452253
## 359 -0.619748924 -0.271394600
## 360  0.484479318 -0.258419685
## 361  0.137323234  0.402658885
## 362  0.677279063 -0.468027915
## 363  1.569191798 -0.324990632
## 364 -0.696431558  0.142034987
## 365 -0.371283677 -0.347928412
## 366 -0.171459484 -0.351391164
## 367 -0.510118334 -0.285977778
## 368  0.663805037 -0.971457197
## 369 -0.164055484 -0.181523245
## 370 -0.869663470 -0.240725882
## 371 -0.035075161  0.387573331
## 372 -0.397415282 -0.229079837
## 373 -0.945243579 -0.209054420
## 374  0.964247801  0.036780440
## 375 -0.368739736  0.503922523
## 376 -1.373515237 -0.173505314
## 377 -0.462933899 -0.787406645
## 378  0.271835930  0.319960047
## 379  0.704812541  0.154968029
# Means of scores for all the PC's classified by Survival status
tabmeansPC <- aggregate(sparrtyp_pca[,2:6],by=list(Survivor=Cancer$Survivor),mean)
tabmeansPC
##   Survivor        PC1         PC2        PC3         PC4         PC5
## 1    Alive -0.1900732 -0.02921761  0.1740706 -0.03610293  0.01331074
## 2     Dead  1.0309052  0.15846840 -0.9441118  0.19581249 -0.07219385
tabmeansPC <- tabmeansPC[rev(order(tabmeansPC$Survivor)),]
tabmeansPC
##   Survivor        PC1         PC2        PC3         PC4         PC5
## 2     Dead  1.0309052  0.15846840 -0.9441118  0.19581249 -0.07219385
## 1    Alive -0.1900732 -0.02921761  0.1740706 -0.03610293  0.01331074
tabfmeans <- t(tabmeansPC[,-1])
tabfmeans
##               2           1
## PC1  1.03090525 -0.19007315
## PC2  0.15846840 -0.02921761
## PC3 -0.94411177  0.17407061
## PC4  0.19581249 -0.03610293
## PC5 -0.07219385  0.01331074
colnames(tabfmeans) <- t(as.vector(tabmeansPC[1]$Survivor))
tabfmeans
##            Dead       Alive
## PC1  1.03090525 -0.19007315
## PC2  0.15846840 -0.02921761
## PC3 -0.94411177  0.17407061
## PC4  0.19581249 -0.03610293
## PC5 -0.07219385  0.01331074
# Standard deviations of scores for all the PC's classified by Survival status
tabsdsPC <- aggregate(sparrtyp_pca[,2:6],by=list(Survivor=Cancer$Survivor),sd)
tabfsds <- t(tabsdsPC[,-1])
colnames(tabfsds) <- t(as.vector(tabsdsPC[1]$Survivor))
tabfsds
##         Alive      Dead
## PC1 1.3032441 1.9907117
## PC2 1.0674058 1.1383653
## PC3 0.8852042 0.9965457
## PC4 0.9481136 1.0060030
## PC5 0.7030204 0.7743521
t.test(PC1~Cancer$Survivor,data=sparrtyp_pca)
## 
##  Welch Two Sample t-test
## 
## data:  PC1 by Cancer$Survivor
## t = -4.5354, df = 67.452, p-value = 2.424e-05
## alternative hypothesis: true difference in means between group Alive and group Dead is not equal to 0
## 95 percent confidence interval:
##  -1.7582650 -0.6836918
## sample estimates:
## mean in group Alive  mean in group Dead 
##          -0.1900732           1.0309052
t.test(PC2~Cancer$Survivor,data=sparrtyp_pca)
## 
##  Welch Two Sample t-test
## 
## data:  PC2 by Cancer$Survivor
## t = -1.1748, df = 77.956, p-value = 0.2437
## alternative hypothesis: true difference in means between group Alive and group Dead is not equal to 0
## 95 percent confidence interval:
##  -0.5057542  0.1303822
## sample estimates:
## mean in group Alive  mean in group Dead 
##         -0.02921761          0.15846840
t.test(PC3~Cancer$Survivor,data=sparrtyp_pca)
## 
##  Welch Two Sample t-test
## 
## data:  PC3 by Cancer$Survivor
## t = 8.0528, df = 75.811, p-value = 8.857e-12
## alternative hypothesis: true difference in means between group Alive and group Dead is not equal to 0
## 95 percent confidence interval:
##  0.8416157 1.3947491
## sample estimates:
## mean in group Alive  mean in group Dead 
##           0.1740706          -0.9441118
t.test(PC4~Cancer$Survivor,data=sparrtyp_pca)
## 
##  Welch Two Sample t-test
## 
## data:  PC4 by Cancer$Survivor
## t = -1.6414, df = 78.171, p-value = 0.1047
## alternative hypothesis: true difference in means between group Alive and group Dead is not equal to 0
## 95 percent confidence interval:
##  -0.51318907  0.04935823
## sample estimates:
## mean in group Alive  mean in group Dead 
##         -0.03610293          0.19581249
t.test(PC5~Cancer$Survivor,data=sparrtyp_pca)
## 
##  Welch Two Sample t-test
## 
## data:  PC5 by Cancer$Survivor
## t = 0.79023, df = 76.646, p-value = 0.4318
## alternative hypothesis: true difference in means between group Alive and group Dead is not equal to 0
## 95 percent confidence interval:
##  -0.1299680  0.3009772
## sample estimates:
## mean in group Alive  mean in group Dead 
##          0.01331074         -0.07219385
## F ratio tests
var.test(PC1~Cancer$Survivor,data=sparrtyp_pca)
## 
##  F test to compare two variances
## 
## data:  PC1 by Cancer$Survivor
## F = 0.42858, num df = 319, denom df = 58, p-value = 3.45e-06
## alternative hypothesis: true ratio of variances is not equal to 1
## 95 percent confidence interval:
##  0.2797709 0.6211181
## sample estimates:
## ratio of variances 
##          0.4285828
var.test(PC2~Cancer$Survivor,data=sparrtyp_pca)
## 
##  F test to compare two variances
## 
## data:  PC2 by Cancer$Survivor
## F = 0.87922, num df = 319, denom df = 58, p-value = 0.4886
## alternative hypothesis: true ratio of variances is not equal to 1
## 95 percent confidence interval:
##  0.5739361 1.2741931
## sample estimates:
## ratio of variances 
##          0.8792165
var.test(PC3~Cancer$Survivor,data=sparrtyp_pca)
## 
##  F test to compare two variances
## 
## data:  PC3 by Cancer$Survivor
## F = 0.78903, num df = 319, denom df = 58, p-value = 0.2112
## alternative hypothesis: true ratio of variances is not equal to 1
## 95 percent confidence interval:
##  0.5150629 1.1434889
## sample estimates:
## ratio of variances 
##          0.7890282
var.test(PC4~Cancer$Survivor,data=sparrtyp_pca)
## 
##  F test to compare two variances
## 
## data:  PC4 by Cancer$Survivor
## F = 0.88822, num df = 319, denom df = 58, p-value = 0.5217
## alternative hypothesis: true ratio of variances is not equal to 1
## 95 percent confidence interval:
##  0.5798156 1.2872462
## sample estimates:
## ratio of variances 
##          0.8882233
var.test(PC5~Cancer$Survivor,data=sparrtyp_pca)
## 
##  F test to compare two variances
## 
## data:  PC5 by Cancer$Survivor
## F = 0.82425, num df = 319, denom df = 58, p-value = 0.306
## alternative hypothesis: true ratio of variances is not equal to 1
## 95 percent confidence interval:
##  0.538055 1.194534
## sample estimates:
## ratio of variances 
##          0.8242499
# Levene's tests (one-sided)
library(car)
## Loading required package: carData
## 
## Attaching package: 'car'
## 
## The following object is masked from 'package:purrr':
## 
##     some
## 
## The following object is masked from 'package:dplyr':
## 
##     recode
(LTPC1 <- leveneTest(PC1~Cancer$Survivor,data=sparrtyp_pca))
## Warning in leveneTest.default(y = y, group = group, ...): group coerced to
## factor.
## Levene's Test for Homogeneity of Variance (center = median)
##        Df F value    Pr(>F)    
## group   1  13.574 0.0002629 ***
##       377                      
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
(p_PC1_1sided <- LTPC1[[3]][1]/2)
## [1] 0.0001314606
(LTPC2 <- leveneTest(PC2~Cancer$Survivor,data=sparrtyp_pca))
## Warning in leveneTest.default(y = y, group = group, ...): group coerced to
## factor.
## Levene's Test for Homogeneity of Variance (center = median)
##        Df F value Pr(>F)
## group   1  1.8085 0.1795
##       377
(p_PC2_1sided=LTPC2[[3]][1]/2)
## [1] 0.08975099
(LTPC3 <- leveneTest(PC3~Cancer$Survivor,data=sparrtyp_pca))
## Warning in leveneTest.default(y = y, group = group, ...): group coerced to
## factor.
## Levene's Test for Homogeneity of Variance (center = median)
##        Df F value Pr(>F)
## group   1  0.8964 0.3444
##       377
(p_PC3_1sided <- LTPC3[[3]][1]/2)
## [1] 0.1721817
(LTPC4 <- leveneTest(PC4~Cancer$Survivor,data=sparrtyp_pca))
## Warning in leveneTest.default(y = y, group = group, ...): group coerced to
## factor.
## Levene's Test for Homogeneity of Variance (center = median)
##        Df F value Pr(>F)
## group   1   0.958 0.3283
##       377
(p_PC4_1sided <- LTPC4[[3]][1]/2)
## [1] 0.1641622
(LTPC5 <- leveneTest(PC5~Cancer$Survivor,data=sparrtyp_pca))
## Warning in leveneTest.default(y = y, group = group, ...): group coerced to
## factor.
## Levene's Test for Homogeneity of Variance (center = median)
##        Df F value Pr(>F)
## group   1  1.7506 0.1866
##       377
(p_PC5_1sided <- LTPC5[[3]][1]/2)
## [1] 0.09330252
# Plotting the scores for the first and second components
plot(sparrtyp_pca$PC1, sparrtyp_pca$PC2,pch=ifelse(sparrtyp_pca$Survivor == "S",1,16),xlab="PC1", ylab="PC2", main="49 sparrows against values for PC1 & PC2")
abline(h=0)
abline(v=0)
legend("bottomleft", legend=c("Survivor","Nonsurvivor"), pch=c(1,16))

plot(eigen_Cancer, xlab = "Component number", ylab = "Component variance", type = "l", main = "Scree diagram")

plot(log(eigen_Cancer), xlab = "Component number",ylab = "log(Component variance)", type="l",main = "Log(eigenvalue) diagram")

print(summary(Cancer_pca))
## Importance of components:
##                          PC1    PC2    PC3    PC4     PC5     PC6
## Standard deviation     1.496 1.0794 0.9892 0.9597 0.71419 0.43317
## Proportion of Variance 0.373 0.1942 0.1631 0.1535 0.08501 0.03127
## Cumulative Proportion  0.373 0.5672 0.7302 0.8837 0.96873 1.00000
diag(cov(Cancer_pca$x))
##       PC1       PC2       PC3       PC4       PC5       PC6 
## 2.2378787 1.1649997 0.9784385 0.9209868 0.5100636 0.1876326
xlim <- range(Cancer_pca$x[,1])
Cancer_pca$x[,1]
##   [1] -1.493744354  0.426322428  1.694207768 -1.767583528  0.043714825
##   [6] -1.028534021 -1.338771984  0.406514411  4.993025728  1.937948477
##  [11] -1.756901401  1.296312778 -0.090142691 -0.076244034  1.004107956
##  [16] -1.005634503 -0.538374841  0.204445317 -0.419443766 -0.252782392
##  [21] -0.036353656  0.504291512 -0.618672209  1.459334722  0.693501261
##  [26]  1.342457422  2.475721782 -1.137184838 -0.082096727 -0.951459346
##  [31]  0.004306142 -1.358590305 -1.790419403 -0.908445651  1.245709794
##  [36] -1.439873416  0.636390371 -1.304428696 -0.097417933 -0.188925650
##  [41]  2.535953943 -1.364589888 -1.095258604  0.018958421 -1.483766860
##  [46]  0.803570710 -0.776759752 -1.440160549  0.550199236 -1.959716237
##  [51]  0.283946083  0.584420507  2.164109035  1.673683848 -1.630123732
##  [56] -1.450559221 -0.534036352 -0.354843129 -1.178588655 -1.248535425
##  [61] -0.944827480 -1.056029210 -0.473763736  1.681009012 -1.312786276
##  [66] -1.639877002  4.455166578 -0.707613499 -1.710632794 -1.171903123
##  [71]  3.302612150  2.121655213  0.528823585 -1.868775707  0.683905846
##  [76]  0.821006546 -0.499967072  0.056071716  0.099588612 -1.638985742
##  [81]  0.865297254 -1.545124764 -0.757282603 -1.494668798 -1.198962297
##  [86]  1.053228198  2.839883593  1.506058603 -1.539415867 -2.166532837
##  [91]  0.893002750 -0.677904182 -0.646604416  1.683330979 -1.509921397
##  [96] -0.135237286  0.027644129 -0.637273583  1.070049729 -0.455435814
## [101]  4.600390311 -0.787145836  0.655142324 -0.428540034 -0.110654721
## [106] -0.734249607  0.296584193 -1.410702952 -0.418905210  0.446752555
## [111] -1.134059417  1.181466882  1.830654533  0.454774207  0.864920996
## [116] -0.897625868  1.357865125 -0.915336154  0.094948933 -0.037442692
## [121] -0.703244230  1.727474232  1.839479021  0.275373090 -0.732974709
## [126] -0.921856464 -0.151799435 -1.471716143 -1.483838817 -0.899242135
## [131] -1.358439633  0.549771469 -1.825714544 -1.466418848  0.713759778
## [136]  0.095641779 -0.311491252 -0.482193479  1.024336162  2.074951928
## [141] -1.891283328 -0.768896963 -0.660225602  0.458314079  0.202499186
## [146] -0.635694229 -1.314850127  2.618727317 -1.867933212 -0.390204192
## [151] -1.169108179 -0.593384345 -1.153893444 -1.299586961 -1.312753509
## [156]  2.158951805 -0.888545794 -1.604599290 -0.695240701  1.698058938
## [161]  0.523091631 -1.639464234 -1.775434759 -1.300191877  0.127243391
## [166]  0.728909729 -0.691130861  4.057107584  0.065928057 -1.537449988
## [171]  0.005212931  1.307010016 -1.400091197 -1.914378275 -1.354059138
## [176]  1.278137221 -0.240072950 -1.192542565  1.517499402  0.419667049
## [181] -1.183491054 -0.049231716 -1.497163756  1.362728567  3.022520941
## [186] -0.646848816  0.841699831 -0.341629561  0.597265999 -1.161264597
## [191] -0.477014120 -2.115125949 -0.991130507 -0.707735717  3.115036491
## [196] -1.696392904  0.151090645  1.330786502  0.296675856 -0.422623151
## [201] -0.318075869 -0.085308348 -1.822877611  1.201683038 -1.807181645
## [206] -1.784093888 -0.078106596 -0.721328123 -0.483839459  0.663630444
## [211]  1.978468906  2.937647970 -0.086636710 -1.481813930  0.623006822
## [216]  1.991882118  0.744165906  0.641119818 -1.586401627  4.773395918
## [221]  2.921320323  0.503935335 -1.241990069 -0.133856941 -1.486223026
## [226] -0.762041381  2.005021660  1.814305601 -1.411373860 -0.324175998
## [231] -0.456860329 -1.210396528  0.367888943 -1.737267642 -1.509987525
## [236] -1.290446225  3.655612544  0.611276361  6.711875034 -1.281390399
## [241]  0.776720455  0.008347450 -0.958826089  1.609087788  0.543831815
## [246] -1.795501728 -2.078996209  0.486998129 -0.821657492 -1.398504155
## [251]  0.526594325  0.120809384 -0.289560811  2.350354264  2.529945185
## [256] -0.594294620 -1.406577585 -1.651971076  0.415871178 -0.286827613
## [261] -0.645411407 -0.628353063 -0.136446586 -1.777655604 -1.357302997
## [266] -1.150407815 -0.854919366  1.748954057 -0.738423976 -0.346935263
## [271]  2.611945346 -0.054669716  0.590763284 -0.771766282  0.287407340
## [276] -1.904210848  1.980934953  4.349982486 -1.601460087  1.110817200
## [281] -1.635586546 -0.910449829  0.979721615 -0.472435837  0.298128461
## [286]  0.876478490  0.030556752  0.489276289  1.167193218  5.639123713
## [291]  0.076038156 -1.306362503 -1.492629535  0.548191410  3.173294742
## [296] -1.711510331 -1.420928885 -0.397038374 -1.338159554  1.238726422
## [301]  0.476798036  0.451358041 -0.410664267  0.631511135  0.606275351
## [306]  3.760469200  0.283257978  1.205872572 -0.547890175  0.675442079
## [311] -0.347420655 -1.082694803 -0.809911038  2.814192996 -1.219216145
## [316] -0.839858529  1.906604890 -1.128786006  4.980287452 -0.396555408
## [321] -1.686147468 -0.771587552  2.121003409  0.183525269 -0.388480855
## [326] -0.270374270 -0.016309255 -1.509365115  1.128006246 -0.013678857
## [331]  0.134239505  0.543266130 -1.694510184 -1.177192240 -0.154704801
## [336] -1.222393212  0.985284375  1.845084419 -1.537001279  0.486580696
## [341] -0.381846642 -1.058469609  1.953784231 -1.632770525 -0.069211481
## [346]  0.924645953 -1.679627649 -0.138978457 -0.306354427 -1.082397105
## [351]  1.560087096  0.213890453 -1.243101129 -1.723673624 -1.845736715
## [356] -0.533908899 -0.621852817 -0.663822556 -1.464448793 -1.523194528
## [361] -0.249284791 -0.978278825  2.298810986 -0.641761160 -1.237501132
## [366] -1.157403928 -0.796933393  2.646899548 -0.178975454 -1.330874437
## [371]  0.785519987  4.528600634 -2.215387412  0.852816653  1.528575274
## [376]  1.052831636  3.308075529  0.145308323 -0.100434292
Cancer_pca$x
##                 PC1          PC2          PC3          PC4          PC5
##   [1,] -1.493744354  1.672703734 -0.797771118 -0.639380539  0.852277723
##   [2,]  0.426322428 -0.124086338 -0.222112841  0.478038848 -0.014925567
##   [3,]  1.694207768 -0.545124348  0.069937198 -1.032701826 -0.039058417
##   [4,] -1.767583528 -0.885302494 -0.030847119 -0.208720400 -0.771910136
##   [5,]  0.043714825 -1.603388200 -0.903121553  0.849669634 -0.078371793
##   [6,] -1.028534021  0.502739380  0.863904840  0.421284750  0.233248754
##   [7,] -1.338771984  0.023023987 -0.740136022  1.021953281  0.038121315
##   [8,]  0.406514411 -0.944219552 -1.935001240  2.169992691  0.548288673
##   [9,]  4.993025728 -0.305103355  0.801778453  0.176933443 -0.724303190
##  [10,]  1.937948477  0.689507346  0.639790414 -2.348269489 -0.376692694
##  [11,] -1.756901401  0.140915113 -1.036789014 -0.816405788 -0.204199065
##  [12,]  1.296312778 -1.473829054  1.127778467 -0.112920985  0.266696937
##  [13,] -0.090142691 -0.016296775 -1.070302648 -0.891412586  0.200775716
##  [14,] -0.076244034  1.581531699 -0.943407970  1.540387096  0.141353261
##  [15,]  1.004107956  1.120512340 -0.515080564 -0.672554789 -1.296448032
##  [16,] -1.005634503  0.998331229 -1.092830786  0.057925043  0.742413832
##  [17,] -0.538374841 -1.839056096  0.934166263 -0.882076640 -0.578346113
##  [18,]  0.204445317  0.244548369  0.249012257  1.256474649  1.134795943
##  [19,] -0.419443766 -0.379535399  1.728764442  0.083365143  0.402986436
##  [20,] -0.252782392  0.344103196  0.155613436 -0.655869450  0.860603335
##  [21,] -0.036353656 -0.349284099  0.645811404  0.425442619  0.372107468
##  [22,]  0.504291512  0.121502823 -0.952996651 -0.061329141  0.135596833
##  [23,] -0.618672209 -1.285043286 -0.036105811 -0.229784303 -0.280109421
##  [24,]  1.459334722 -1.104003050  1.630015919 -0.538883137  1.064729564
##  [25,]  0.693501261  3.217631237  1.088615995 -0.680914229 -2.330312186
##  [26,]  1.342457422  2.945510521  0.104659090 -0.694326558 -0.785747318
##  [27,]  2.475721782  2.107120006  1.821692902  0.042150966 -2.125689786
##  [28,] -1.137184838 -0.018509243  0.662500068  1.019754895  0.143564512
##  [29,] -0.082096727  0.062026127 -0.404849247 -0.143815038  0.043817854
##  [30,] -0.951459346 -0.397603334  0.033425845 -1.324785280  0.016907630
##  [31,]  0.004306142 -1.599200390 -0.821234717  0.828802331 -0.096628489
##  [32,] -1.358590305 -0.557530387 -1.182191573  0.826013095 -0.330970546
##  [33,] -1.790419403 -0.472260893  0.282426323 -0.357402908 -0.542183270
##  [34,] -0.908445651  0.994824271 -0.546660828 -0.042005466  0.292432820
##  [35,]  1.245709794  0.857794242 -1.178327309  1.397760831 -0.230660457
##  [36,] -1.439873416 -0.186081367  0.144133667  0.662537801 -0.393665514
##  [37,]  0.636390371  0.900377415 -1.197745317  0.553485818  0.437914429
##  [38,] -1.304428696  0.097530771  1.328492259  0.221100925 -0.155155562
##  [39,] -0.097417933 -0.858136005  0.513336501  0.257353363  0.029439452
##  [40,] -0.188925650 -0.025716107  1.521237025 -0.147451873 -0.286733286
##  [41,]  2.535953943 -0.283072938 -1.273811462 -0.496124138 -0.691155605
##  [42,] -1.364589888  0.380987232 -0.926166470 -0.409214549 -0.084453563
##  [43,] -1.095258604 -1.245692755 -0.025636708 -0.959504567 -0.544787256
##  [44,]  0.018958421  0.185171532  0.594724325 -0.026225609 -0.312285920
##  [45,] -1.483766860  0.205593899 -0.521531513  0.532329976 -0.202487124
##  [46,]  0.803570710 -0.823728790  0.269737583 -1.940110944 -0.213877418
##  [47,] -0.776759752  0.318065419 -0.898736044  2.118307298  0.308120927
##  [48,] -1.440160549  0.277491231 -0.933452622 -0.172656258  0.076695703
##  [49,]  0.550199236  0.443259288  0.544534206 -0.061726221 -0.634281043
##  [50,] -1.959716237  0.269905907 -0.358261698 -1.104900464 -0.742921582
##  [51,]  0.283946083 -0.215989222  0.718462913  1.705505213  0.429398197
##  [52,]  0.584420507 -1.170636855 -0.658910102 -2.000608348  0.454750957
##  [53,]  2.164109035 -2.375151885  0.202704168 -1.926001263  0.605914036
##  [54,]  1.673683848 -0.438611018 -0.189966395 -1.566014043  1.244480037
##  [55,] -1.630123732  0.631351549 -0.019980046  0.212113815  0.215871580
##  [56,] -1.450559221  0.201501035 -0.069005014  0.333630589  0.063005452
##  [57,] -0.534036352  0.291756051  0.624478817 -1.023860005  0.669994233
##  [58,] -0.354843129  3.274197111  2.410035980  0.361353654  2.502769179
##  [59,] -1.178588655  0.226034827  0.171909908  0.786762124  0.247357475
##  [60,] -1.248535425  0.638963394  0.202025885  0.279803670  0.179044984
##  [61,] -0.944827480  1.241989527  0.467351263  0.104831170  0.693575290
##  [62,] -1.056029210  0.031887224 -0.922233051  1.020017722  0.191600412
##  [63,] -0.473763736 -1.839525046  0.381440310  1.043813308 -0.465299021
##  [64,]  1.681009012 -0.528168820  0.166784745 -1.236306623  1.216190250
##  [65,] -1.312786276  0.965097163 -0.969708882 -0.635102168  0.024970627
##  [66,] -1.639877002 -0.931529988  1.401477586  0.658502060 -0.668767345
##  [67,]  4.455166578  1.087532562  0.124772958  2.053348449 -1.489900944
##  [68,] -0.707613499  0.590986037  1.179291019  1.595111891  0.263308423
##  [69,] -1.710632794 -0.549715482 -0.153074842 -0.100695874 -0.540451474
##  [70,] -1.171903123  0.100583865  0.469100757  0.412780064 -0.339388614
##  [71,]  3.302612150 -1.737283578  1.502810946 -1.179097587 -0.118238924
##  [72,]  2.121655213  2.644141124 -2.473204090 -0.044893038 -1.314192531
##  [73,]  0.528823585 -0.636078944  0.137430927  2.495082814  0.843161685
##  [74,] -1.868775707  0.569029628  0.581800057 -1.084485611  0.002065102
##  [75,]  0.683905846  1.767290796  0.241693051 -1.337566812 -1.608284497
##  [76,]  0.821006546 -1.188104492  0.917466077 -1.089980478  0.637354405
##  [77,] -0.499967072 -0.063567628 -0.217092609 -1.242667319 -0.300754296
##  [78,]  0.056071716 -1.653376800  1.664161542  0.435774870 -0.079376450
##  [79,]  0.099588612 -1.161140621  0.358003056 -0.058098223  0.191212303
##  [80,] -1.638985742  0.150875793 -1.403816856 -0.700686152 -0.135813445
##  [81,]  0.865297254  1.214733944  1.463461173 -0.297882350 -1.014695877
##  [82,] -1.545124764  0.127252910 -0.935729044 -0.793110208 -0.096332740
##  [83,] -0.757282603 -0.365269832 -0.559376514 -1.125365040 -0.112495907
##  [84,] -1.494668798 -0.862217669 -1.017557513  0.729371690 -0.585327071
##  [85,] -1.198962297  0.090483632 -0.244225721  0.803338834  0.150630291
##  [86,]  1.053228198  0.023027292  0.260206980  0.703883631 -1.086933498
##  [87,]  2.839883593 -2.296312935  0.510353279 -0.693661524  0.066738128
##  [88,]  1.506058603 -1.812772768  0.528733408 -0.767001468  0.643656650
##  [89,] -1.539415867 -0.136768478  0.768955037 -0.049503375 -0.188258747
##  [90,] -2.166532837  0.071753733  0.343483494 -0.898166612 -0.445936393
##  [91,]  0.893002750 -1.772886261  0.734063638 -0.797845672  0.341156668
##  [92,] -0.677904182 -0.104397875  0.169469929  2.673756815  0.405882517
##  [93,] -0.646604416 -0.740495104  0.063231982 -1.095809541 -0.767513218
##  [94,]  1.683330979  1.567742424 -0.698706197  1.431672587 -1.080548515
##  [95,] -1.509921397  0.297490480  0.490010821 -0.323083740 -0.437095352
##  [96,] -0.135237286  0.293266912 -1.015571227 -0.225694168  0.642455326
##  [97,]  0.027644129 -1.133291443 -1.997458759  1.032137750 -0.070625404
##  [98,] -0.637273583 -0.513850978 -0.306967375 -0.684532247  0.140054208
##  [99,]  1.070049729 -2.036508976 -0.316339810 -0.094341352 -0.094161935
## [100,] -0.455435814  0.089328755 -1.403983913 -1.027093674  0.560281943
## [101,]  4.600390311  2.244846920  0.532264308  1.259266636 -1.010942778
## [102,] -0.787145836  1.086091949  0.549806202  1.093912587  0.984179992
## [103,]  0.655142324 -1.683984928 -2.308143986  2.208715115  0.240582243
## [104,] -0.428540034 -0.840500324 -1.048098702 -0.027665882  0.077046929
## [105,] -0.110654721 -0.123171275 -0.175937919  0.338031509  0.196792323
## [106,] -0.734249607 -1.236231879 -1.090037416 -0.386975718 -0.336972535
## [107,]  0.296584193 -0.577728068 -2.014640498  0.588158511  0.632602330
## [108,] -1.410702952  0.429684625 -0.958296105 -0.866024725 -0.101651534
## [109,] -0.418905210 -1.232525386  1.863199813  1.081316900 -0.304585111
## [110,]  0.446752555  1.508585940 -0.342268303 -0.736468382  1.406332814
## [111,] -1.134059417  0.782686222 -0.521004605 -0.152263500 -0.210024740
## [112,]  1.181466882 -2.299898160  0.735344703  0.997333267 -0.237945040
## [113,]  1.830654533  1.883074076  0.954309940  0.626252247  0.685943765
## [114,]  0.454774207 -0.643039459  0.237045213  0.759165544  0.470129822
## [115,]  0.864920996 -1.531113286  1.149483739 -0.984234084 -0.541097522
## [116,] -0.897625868  0.218458064 -0.870977930  0.772271080 -0.128040261
## [117,]  1.357865125 -1.941049776  0.946671254 -0.674767960  0.499517827
## [118,] -0.915336154  1.327339693  0.352068802 -1.370754921 -1.073206670
## [119,]  0.094948933 -0.356826249  1.052712045  0.237447671  0.183785081
## [120,] -0.037442692 -0.108870167 -0.518461408  0.323952099  0.490323176
## [121,] -0.703244230 -0.760629115  0.236405707 -1.666145723 -0.328854978
## [122,]  1.727474232 -1.256161661  0.911292089  0.280268540  0.754418800
## [123,]  1.839479021  0.845697621 -0.141543565  0.392072998 -1.461521820
## [124,]  0.275373090  0.726740366  0.643511448 -0.752337791  0.616212060
## [125,] -0.732974709  1.225314046 -0.703247765  0.876777966  0.813571603
## [126,] -0.921856464  0.796384898 -2.658215899  0.486234753  0.662707828
## [127,] -0.151799435 -0.761905068  1.710990722  1.051731292  0.112226358
## [128,] -1.471716143 -0.654343538 -1.425218658  0.191711126 -0.481284081
## [129,] -1.483838817 -0.227422742  0.005677556  0.103891666 -0.469159558
## [130,] -0.899242135  0.043994478  0.476955011  1.186170494 -0.191676482
## [131,] -1.358439633  0.497908624 -1.167958845  0.193782726  0.263406749
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## [326,] -0.270374270  0.372642009  0.619830911 -1.148519958 -0.407017698
## [327,] -0.016309255 -0.272150173  1.123754077 -0.347941297 -0.103237180
## [328,] -1.509365115 -1.227221931  0.110956778  1.437386493 -0.758506439
## [329,]  1.128006246 -1.746278013  0.499382396 -1.619420542  0.555724903
## [330,] -0.013678857  0.097843119  0.408072714 -0.795855347 -1.175223096
## [331,]  0.134239505  0.261168839  1.687827776  0.217195174  1.082628063
## [332,]  0.543266130  0.289044087 -1.889627887  1.415180585  1.063577278
## [333,] -1.694510184 -0.384164773  0.978956440 -0.619188118 -0.943767153
## [334,] -1.177192240  0.755347480 -0.072837954  0.262273753  0.532730202
## [335,] -0.154704801 -0.482019591 -0.130393501  0.108703255  0.455787032
## [336,] -1.222393212 -0.140605864  0.470903440  0.854635087 -0.236602493
## [337,]  0.985284375 -2.085350193 -0.309169317 -0.356636930  0.209646403
## [338,]  1.845084419 -1.284127961 -0.428328294 -1.460289251  0.838247554
## [339,] -1.537001279  1.111570387  0.652894920 -1.060718845 -0.002140100
## [340,]  0.486580696 -0.438599188 -0.143918334  0.966749788  0.107166844
## [341,] -0.381846642 -0.365594889  0.626052636  0.039508221 -0.092159877
## [342,] -1.058469609  1.839970213 -0.254329772 -0.731552164 -0.827823834
## [343,]  1.953784231 -1.229071105  0.160259672  0.867246394  1.295990204
## [344,] -1.632770525 -0.310017947  0.586575867  0.624972262 -0.312659105
## [345,] -0.069211481  1.179578849 -0.019456868 -1.025693279  0.424192027
## [346,]  0.924645953  0.318200997 -0.038558980 -0.176342543 -1.278270521
## [347,] -1.679627649 -0.870249748  1.201962925  0.638583744 -0.657934688
## [348,] -0.138978457 -0.327879510  1.445999742  0.018109114  0.324021275
## [349,] -0.306354427  2.443421548  0.256738595  0.723881262  0.004780055
## [350,] -1.082397105  0.511694553  0.396630701  0.376171916  0.200267508
## [351,]  1.560087096 -0.172608049  2.042673531  0.001387343  0.943307040
## [352,]  0.213890453  0.121650120 -0.363220480  0.143134581  0.251009799
## [353,] -1.243101129 -0.469575151 -1.404226113  1.148855158 -0.206147146
## [354,] -1.723673624 -0.628891973  1.215101216  0.822337346 -0.530509884
## [355,] -1.845736715 -1.246640827  1.218806001  0.592440275 -0.970712299
## [356,] -0.533908899  0.509703545 -1.010222476 -1.067833304  0.770760459
## [357,] -0.621852817  1.060330174 -0.185420284  0.974853637  0.788314716
## [358,] -0.663822556 -0.698693563 -1.437208451 -1.000964685 -0.267520648
## [359,] -1.464448793 -0.997923794  0.090438438  0.991886193 -0.619748924
## [360,] -1.523194528  1.088366756 -0.015584201 -1.071387626  0.484479318
## [361,] -0.249284791 -0.495162923 -0.888175969  0.194375075  0.137323234
## [362,] -0.978278825  0.745196276  1.673492426  0.624652999  0.677279063
## [363,]  2.298810986 -0.090143085 -0.751106742 -0.561856912  1.569191798
## [364,] -0.641761160 -1.573225212  0.960424847 -0.179437036 -0.696431558
## [365,] -1.237501132 -0.412442737  1.793811573  1.137104529 -0.371283677
## [366,] -1.157403928  0.923508573 -0.442026074 -0.884941552 -0.171459484
## [367,] -0.796933393  1.222876039  0.723404723 -0.237384378 -0.510118334
## [368,]  2.646899548  0.301553970  0.690593527 -2.443750630  0.663805037
## [369,] -0.178975454 -0.138624086  1.105283992 -1.499072183 -0.164055484
## [370,] -1.330874437  0.769296425 -0.127097036 -1.223980155 -0.869663470
## [371,]  0.785519987  2.132318925  0.981263612 -0.639682484 -0.035075161
## [372,]  4.528600634 -0.995996130  0.568209680 -0.292649916 -0.397415282
## [373,] -2.215387412 -0.717213408  0.437807288 -1.098624561 -0.945243579
## [374,]  0.852816653  0.697424945 -0.415247520  0.859928559  0.964247801
## [375,]  1.528575274  1.579100810  0.424898608  1.740887715 -0.368739736
## [376,]  1.052831636  0.469776583  0.746395631 -0.477473960 -1.373515237
## [377,]  3.308075529 -0.637217047 -0.361014725 -0.281269186 -0.462933899
## [378,]  0.145308323 -0.337470348  1.183817291  1.285154406  0.271835930
## [379,] -0.100434292 -0.148112235  0.886936726  0.259148546  0.704812541
##                 PC6
##   [1,]  0.116709537
##   [2,]  0.110173000
##   [3,]  0.151011377
##   [4,] -0.343807479
##   [5,] -0.068417317
##   [6,] -0.420280958
##   [7,]  0.014839886
##   [8,]  0.336718257
##   [9,] -0.045952454
##  [10,]  1.939826284
##  [11,] -0.146897222
##  [12,]  0.183314250
##  [13,]  0.114162471
##  [14,] -0.102727402
##  [15,]  0.196911289
##  [16,] -0.296960713
##  [17,] -0.346683316
##  [18,]  0.385229903
##  [19,]  0.250212417
##  [20,]  0.210997273
##  [21,]  0.178758339
##  [22,] -0.003801151
##  [23,]  0.217319459
##  [24,] -0.187966712
##  [25,] -0.249408299
##  [26,]  0.582504343
##  [27,] -0.264956027
##  [28,] -0.324073726
##  [29,]  0.392690074
##  [30,]  0.433561922
##  [31,] -0.044052794
##  [32,] -0.172924722
##  [33,] -0.273046392
##  [34,] -0.339264995
##  [35,]  0.377235819
##  [36,] -0.090271827
##  [37,]  0.414287669
##  [38,] -0.393701821
##  [39,]  0.033505637
##  [40,]  0.354862667
##  [41,]  0.077217544
##  [42,] -0.251343699
##  [43,]  0.437209594
##  [44,]  0.418033744
##  [45,]  0.092143326
##  [46,]  0.453442755
##  [47,]  0.025217332
##  [48,] -0.198309910
##  [49,]  0.187074835
##  [50,]  0.063584865
##  [51,]  0.411945392
##  [52,]  0.347020693
##  [53,] -1.602200768
##  [54,] -0.297652746
##  [55,]  0.140534670
##  [56,] -0.120117267
##  [57,]  0.295188323
##  [58,] -0.436240290
##  [59,] -0.241532009
##  [60,] -0.152644965
##  [61,] -0.340782009
##  [62,] -0.237639469
##  [63,]  0.300926071
##  [64,] -0.253457399
##  [65,] -0.123036265
##  [66,] -0.318934216
##  [67,]  0.157579795
##  [68,] -0.260813996
##  [69,] -0.245354609
##  [70,] -0.305254302
##  [71,] -1.882250425
##  [72,]  0.409598000
##  [73,]  0.232202465
##  [74,] -0.149057573
##  [75,]  0.545903188
##  [76,]  0.277588617
##  [77,]  0.361912198
##  [78,] -0.478016137
##  [79,] -0.412381253
##  [80,] -0.183130748
##  [81,]  0.233456245
##  [82,] -0.356154388
##  [83,]  0.449569521
##  [84,] -0.185788498
##  [85,] -0.219609958
##  [86,] -0.001711114
##  [87,] -1.559617792
##  [88,] -0.428893296
##  [89,] -0.349853393
##  [90,]  0.067731920
##  [91,]  0.142796842
##  [92,] -0.180830638
##  [93,]  0.315292384
##  [94,]  0.557663845
##  [95,] -0.172373827
##  [96,]  0.407727459
##  [97,]  0.327538602
##  [98,]  0.346056104
##  [99,]  2.163269668
## [100,]  0.345529449
## [101,]  0.138719045
## [102,] -0.279523523
## [103,] -0.084975054
## [104,]  0.337408982
## [105,]  0.436700603
## [106,]  0.388716289
## [107,]  0.023800405
## [108,] -0.344894615
## [109,]  0.380430817
## [110,]  0.059212100
## [111,] -0.160062648
## [112,]  0.451808896
## [113,] -0.328134576
## [114,] -0.232509061
## [115,]  0.417691744
## [116,] -0.283499777
## [117,] -0.334241319
## [118,] -0.354492127
## [119,]  0.016626218
## [120,]  0.329368287
## [121,]  0.014802916
## [122,]  1.788209994
## [123,] -0.225290106
## [124,] -0.049381001
## [125,] -0.176037238
## [126,] -0.147416810
## [127,]  0.274931744
## [128,] -0.288402296
## [129,] -0.238830171
## [130,] -0.321394130
## [131,] -0.060804904
## [132,] -0.198430755
## [133,] -0.201882037
## [134,] -0.416230299
## [135,] -0.104823016
## [136,] -0.259292999
## [137,]  0.309515655
## [138,]  0.473433423
## [139,] -0.224455247
## [140,] -0.113549634
## [141,] -0.029270791
## [142,] -0.408139727
## [143,] -0.249679273
## [144,]  0.052432954
## [145,]  0.123609326
## [146,]  0.110721474
## [147,]  0.039482206
## [148,] -0.055563924
## [149,] -0.301541438
## [150,]  0.339761189
## [151,] -0.143565175
## [152,]  0.495882321
## [153,] -0.338275303
## [154,] -0.259013852
## [155,] -0.268105530
## [156,] -0.980893416
## [157,] -0.246803124
## [158,] -0.078306763
## [159,]  0.382030122
## [160,]  0.087323777
## [161,]  0.376505108
## [162,]  0.053401289
## [163,] -0.338300621
## [164,] -0.183747770
## [165,]  0.432642111
## [166,]  0.187719391
## [167,] -0.323645603
## [168,]  0.829006715
## [169,]  0.043491740
## [170,] -0.248046133
## [171,] -0.060255793
## [172,] -0.083545793
## [173,] -0.167508321
## [174,] -0.089468938
## [175,] -0.143831223
## [176,]  0.323860642
## [177,] -0.174432941
## [178,] -0.239734115
## [179,]  0.497289814
## [180,] -0.327540210
## [181,] -0.151688764
## [182,]  0.197182238
## [183,] -0.042715485
## [184,]  0.044010655
## [185,] -0.925270972
## [186,]  0.322942444
## [187,] -0.036587651
## [188,]  0.356359819
## [189,]  0.423139332
## [190,] -0.257850948
## [191,]  0.463686146
## [192,] -0.032295644
## [193,] -0.221120598
## [194,]  0.347410914
## [195,] -0.102882758
## [196,] -0.052886406
## [197,]  0.099771649
## [198,]  0.161046943
## [199,]  0.245795874
## [200,]  0.272924190
## [201,]  0.339839246
## [202,]  0.395294558
## [203,] -0.065386536
## [204,]  0.561844444
## [205,] -0.271407182
## [206,] -0.059059407
## [207,]  0.083045883
## [208,]  0.377344777
## [209,]  0.334594979
## [210,]  2.210117773
## [211,] -0.225352991
## [212,]  0.659498155
## [213,]  0.005821771
## [214,] -0.246898562
## [215,]  0.168733702
## [216,] -0.366893261
## [217,] -0.293117425
## [218,]  0.423293245
## [219,] -0.277523269
## [220,]  0.108760866
## [221,]  0.070710680
## [222,]  0.163384108
## [223,] -0.232906221
## [224,]  0.408184032
## [225,] -0.300209061
## [226,] -0.343281023
## [227,]  0.380266460
## [228,]  0.475769439
## [229,] -0.240418547
## [230,]  0.118544474
## [231,]  0.411577815
## [232,] -0.017746096
## [233,] -0.022662183
## [234,] -0.215224961
## [235,] -0.336453644
## [236,] -0.208327609
## [237,]  0.415886191
## [238,]  0.260849310
## [239,] -0.336942900
## [240,] -0.122484819
## [241,] -0.025660118
## [242,]  0.330693931
## [243,]  0.187450418
## [244,]  0.092254142
## [245,] -0.103389100
## [246,] -0.135338511
## [247,] -0.081072198
## [248,]  0.345962874
## [249,] -0.250967381
## [250,] -0.344899324
## [251,] -0.429960219
## [252,] -0.282830186
## [253,]  0.174435063
## [254,] -0.002994835
## [255,] -1.217412358
## [256,]  0.360421127
## [257,] -0.146287428
## [258,] -0.133025274
## [259,] -0.126146676
## [260,]  0.220778323
## [261,]  0.108029807
## [262,]  0.349752615
## [263,]  0.200005121
## [264,] -0.101933578
## [265,] -0.161334026
## [266,]  0.285586865
## [267,] -0.238563544
## [268,]  0.083679922
## [269,]  0.509906873
## [270,] -0.146139621
## [271,]  0.334416111
## [272,]  0.473647831
## [273,]  0.136442835
## [274,] -0.251405937
## [275,]  0.114366181
## [276,]  0.048022334
## [277,] -1.054946234
## [278,] -0.700681151
## [279,] -0.434292485
## [280,]  0.255500421
## [281,] -0.124820953
## [282,] -0.258508925
## [283,]  0.519297048
## [284,]  0.418680932
## [285,] -0.218443452
## [286,] -0.216123751
## [287,]  0.115923969
## [288,] -0.027866918
## [289,] -0.058716464
## [290,] -2.000384525
## [291,]  0.277974900
## [292,] -0.293421787
## [293,] -0.259635342
## [294,]  0.059625913
## [295,]  0.971487465
## [296,] -0.150615259
## [297,] -0.400937784
## [298,]  0.238954410
## [299,] -0.144937084
## [300,]  0.201952185
## [301,] -0.447834040
## [302,]  0.281901496
## [303,] -0.203869133
## [304,] -0.134202490
## [305,] -0.059036104
## [306,] -1.689975498
## [307,]  0.458648969
## [308,]  0.521154125
## [309,]  0.178933466
## [310,]  0.097184547
## [311,]  0.178727506
## [312,] -0.114849810
## [313,] -0.177928676
## [314,]  0.278091472
## [315,] -0.424718686
## [316,]  0.421376781
## [317,] -0.381796482
## [318,] -0.221941061
## [319,] -0.754255469
## [320,]  0.249838558
## [321,] -0.111526776
## [322,] -0.207650126
## [323,] -0.362767449
## [324,]  0.207891984
## [325,]  0.340268457
## [326,]  0.368766457
## [327,]  0.012058601
## [328,] -0.149559490
## [329,]  1.463155184
## [330,]  0.382942476
## [331,] -0.032112095
## [332,]  0.397084457
## [333,] -0.354911460
## [334,] -0.233823936
## [335,]  0.146812456
## [336,] -0.250028422
## [337,]  0.205107833
## [338,] -0.667916271
## [339,] -0.159417162
## [340,]  0.044940196
## [341,]  0.444365443
## [342,]  0.218371896
## [343,] -0.083864131
## [344,] -0.066718642
## [345,]  0.460637350
## [346,]  0.010040209
## [347,] -0.249703684
## [348,]  0.069849151
## [349,]  0.133553509
## [350,] -0.337335972
## [351,]  0.358285729
## [352,]  0.221064477
## [353,] -0.125296735
## [354,] -0.070458295
## [355,] -0.224997131
## [356,]  0.501370980
## [357,] -0.349367892
## [358,]  0.380452253
## [359,] -0.271394600
## [360,] -0.258419685
## [361,]  0.402658885
## [362,] -0.468027915
## [363,] -0.324990632
## [364,]  0.142034987
## [365,] -0.347928412
## [366,] -0.351391164
## [367,] -0.285977778
## [368,] -0.971457197
## [369,] -0.181523245
## [370,] -0.240725882
## [371,]  0.387573331
## [372,] -0.229079837
## [373,] -0.209054420
## [374,]  0.036780440
## [375,]  0.503922523
## [376,] -0.173505314
## [377,] -0.787406645
## [378,]  0.319960047
## [379,]  0.154968029
plot(Cancer_pca$x,xlim=xlim,ylim=xlim)

Cancer_pca$rotation[,1]
##                    Age                  Stage             Tumor Size 
##             -0.2153849              0.5628689              0.5822135 
## Regional Node Examined  Reginol Node Positive        Survival Months 
##              0.2375181              0.4590407             -0.1751633
Cancer_pca$rotation
##                               PC1         PC2         PC3         PC4
## Age                    -0.2153849  0.21608166 -0.34917081 -0.88535662
## Stage                   0.5628689 -0.32693628  0.06177527 -0.24457235
## Tumor Size              0.5822135 -0.28223117 -0.01433325 -0.21375444
## Regional Node Examined  0.2375181  0.75305159  0.21117279  0.02093686
## Reginol Node Positive   0.4590407  0.43924020  0.01680220  0.01827332
## Survival Months        -0.1751633 -0.08214803  0.91059423 -0.33145859
##                                PC5          PC6
## Age                    -0.03346239  0.004663803
## Stage                   0.18847337  0.690751203
## Tumor Size              0.13490974 -0.719218983
## Regional Node Examined  0.57570300 -0.005676451
## Reginol Node Positive  -0.77028208  0.048979548
## Survival Months        -0.14279002 -0.055980895
plot(Cancer[,-1])

Cancer_pca$x
##                 PC1          PC2          PC3          PC4          PC5
##   [1,] -1.493744354  1.672703734 -0.797771118 -0.639380539  0.852277723
##   [2,]  0.426322428 -0.124086338 -0.222112841  0.478038848 -0.014925567
##   [3,]  1.694207768 -0.545124348  0.069937198 -1.032701826 -0.039058417
##   [4,] -1.767583528 -0.885302494 -0.030847119 -0.208720400 -0.771910136
##   [5,]  0.043714825 -1.603388200 -0.903121553  0.849669634 -0.078371793
##   [6,] -1.028534021  0.502739380  0.863904840  0.421284750  0.233248754
##   [7,] -1.338771984  0.023023987 -0.740136022  1.021953281  0.038121315
##   [8,]  0.406514411 -0.944219552 -1.935001240  2.169992691  0.548288673
##   [9,]  4.993025728 -0.305103355  0.801778453  0.176933443 -0.724303190
##  [10,]  1.937948477  0.689507346  0.639790414 -2.348269489 -0.376692694
##  [11,] -1.756901401  0.140915113 -1.036789014 -0.816405788 -0.204199065
##  [12,]  1.296312778 -1.473829054  1.127778467 -0.112920985  0.266696937
##  [13,] -0.090142691 -0.016296775 -1.070302648 -0.891412586  0.200775716
##  [14,] -0.076244034  1.581531699 -0.943407970  1.540387096  0.141353261
##  [15,]  1.004107956  1.120512340 -0.515080564 -0.672554789 -1.296448032
##  [16,] -1.005634503  0.998331229 -1.092830786  0.057925043  0.742413832
##  [17,] -0.538374841 -1.839056096  0.934166263 -0.882076640 -0.578346113
##  [18,]  0.204445317  0.244548369  0.249012257  1.256474649  1.134795943
##  [19,] -0.419443766 -0.379535399  1.728764442  0.083365143  0.402986436
##  [20,] -0.252782392  0.344103196  0.155613436 -0.655869450  0.860603335
##  [21,] -0.036353656 -0.349284099  0.645811404  0.425442619  0.372107468
##  [22,]  0.504291512  0.121502823 -0.952996651 -0.061329141  0.135596833
##  [23,] -0.618672209 -1.285043286 -0.036105811 -0.229784303 -0.280109421
##  [24,]  1.459334722 -1.104003050  1.630015919 -0.538883137  1.064729564
##  [25,]  0.693501261  3.217631237  1.088615995 -0.680914229 -2.330312186
##  [26,]  1.342457422  2.945510521  0.104659090 -0.694326558 -0.785747318
##  [27,]  2.475721782  2.107120006  1.821692902  0.042150966 -2.125689786
##  [28,] -1.137184838 -0.018509243  0.662500068  1.019754895  0.143564512
##  [29,] -0.082096727  0.062026127 -0.404849247 -0.143815038  0.043817854
##  [30,] -0.951459346 -0.397603334  0.033425845 -1.324785280  0.016907630
##  [31,]  0.004306142 -1.599200390 -0.821234717  0.828802331 -0.096628489
##  [32,] -1.358590305 -0.557530387 -1.182191573  0.826013095 -0.330970546
##  [33,] -1.790419403 -0.472260893  0.282426323 -0.357402908 -0.542183270
##  [34,] -0.908445651  0.994824271 -0.546660828 -0.042005466  0.292432820
##  [35,]  1.245709794  0.857794242 -1.178327309  1.397760831 -0.230660457
##  [36,] -1.439873416 -0.186081367  0.144133667  0.662537801 -0.393665514
##  [37,]  0.636390371  0.900377415 -1.197745317  0.553485818  0.437914429
##  [38,] -1.304428696  0.097530771  1.328492259  0.221100925 -0.155155562
##  [39,] -0.097417933 -0.858136005  0.513336501  0.257353363  0.029439452
##  [40,] -0.188925650 -0.025716107  1.521237025 -0.147451873 -0.286733286
##  [41,]  2.535953943 -0.283072938 -1.273811462 -0.496124138 -0.691155605
##  [42,] -1.364589888  0.380987232 -0.926166470 -0.409214549 -0.084453563
##  [43,] -1.095258604 -1.245692755 -0.025636708 -0.959504567 -0.544787256
##  [44,]  0.018958421  0.185171532  0.594724325 -0.026225609 -0.312285920
##  [45,] -1.483766860  0.205593899 -0.521531513  0.532329976 -0.202487124
##  [46,]  0.803570710 -0.823728790  0.269737583 -1.940110944 -0.213877418
##  [47,] -0.776759752  0.318065419 -0.898736044  2.118307298  0.308120927
##  [48,] -1.440160549  0.277491231 -0.933452622 -0.172656258  0.076695703
##  [49,]  0.550199236  0.443259288  0.544534206 -0.061726221 -0.634281043
##  [50,] -1.959716237  0.269905907 -0.358261698 -1.104900464 -0.742921582
##  [51,]  0.283946083 -0.215989222  0.718462913  1.705505213  0.429398197
##  [52,]  0.584420507 -1.170636855 -0.658910102 -2.000608348  0.454750957
##  [53,]  2.164109035 -2.375151885  0.202704168 -1.926001263  0.605914036
##  [54,]  1.673683848 -0.438611018 -0.189966395 -1.566014043  1.244480037
##  [55,] -1.630123732  0.631351549 -0.019980046  0.212113815  0.215871580
##  [56,] -1.450559221  0.201501035 -0.069005014  0.333630589  0.063005452
##  [57,] -0.534036352  0.291756051  0.624478817 -1.023860005  0.669994233
##  [58,] -0.354843129  3.274197111  2.410035980  0.361353654  2.502769179
##  [59,] -1.178588655  0.226034827  0.171909908  0.786762124  0.247357475
##  [60,] -1.248535425  0.638963394  0.202025885  0.279803670  0.179044984
##  [61,] -0.944827480  1.241989527  0.467351263  0.104831170  0.693575290
##  [62,] -1.056029210  0.031887224 -0.922233051  1.020017722  0.191600412
##  [63,] -0.473763736 -1.839525046  0.381440310  1.043813308 -0.465299021
##  [64,]  1.681009012 -0.528168820  0.166784745 -1.236306623  1.216190250
##  [65,] -1.312786276  0.965097163 -0.969708882 -0.635102168  0.024970627
##  [66,] -1.639877002 -0.931529988  1.401477586  0.658502060 -0.668767345
##  [67,]  4.455166578  1.087532562  0.124772958  2.053348449 -1.489900944
##  [68,] -0.707613499  0.590986037  1.179291019  1.595111891  0.263308423
##  [69,] -1.710632794 -0.549715482 -0.153074842 -0.100695874 -0.540451474
##  [70,] -1.171903123  0.100583865  0.469100757  0.412780064 -0.339388614
##  [71,]  3.302612150 -1.737283578  1.502810946 -1.179097587 -0.118238924
##  [72,]  2.121655213  2.644141124 -2.473204090 -0.044893038 -1.314192531
##  [73,]  0.528823585 -0.636078944  0.137430927  2.495082814  0.843161685
##  [74,] -1.868775707  0.569029628  0.581800057 -1.084485611  0.002065102
##  [75,]  0.683905846  1.767290796  0.241693051 -1.337566812 -1.608284497
##  [76,]  0.821006546 -1.188104492  0.917466077 -1.089980478  0.637354405
##  [77,] -0.499967072 -0.063567628 -0.217092609 -1.242667319 -0.300754296
##  [78,]  0.056071716 -1.653376800  1.664161542  0.435774870 -0.079376450
##  [79,]  0.099588612 -1.161140621  0.358003056 -0.058098223  0.191212303
##  [80,] -1.638985742  0.150875793 -1.403816856 -0.700686152 -0.135813445
##  [81,]  0.865297254  1.214733944  1.463461173 -0.297882350 -1.014695877
##  [82,] -1.545124764  0.127252910 -0.935729044 -0.793110208 -0.096332740
##  [83,] -0.757282603 -0.365269832 -0.559376514 -1.125365040 -0.112495907
##  [84,] -1.494668798 -0.862217669 -1.017557513  0.729371690 -0.585327071
##  [85,] -1.198962297  0.090483632 -0.244225721  0.803338834  0.150630291
##  [86,]  1.053228198  0.023027292  0.260206980  0.703883631 -1.086933498
##  [87,]  2.839883593 -2.296312935  0.510353279 -0.693661524  0.066738128
##  [88,]  1.506058603 -1.812772768  0.528733408 -0.767001468  0.643656650
##  [89,] -1.539415867 -0.136768478  0.768955037 -0.049503375 -0.188258747
##  [90,] -2.166532837  0.071753733  0.343483494 -0.898166612 -0.445936393
##  [91,]  0.893002750 -1.772886261  0.734063638 -0.797845672  0.341156668
##  [92,] -0.677904182 -0.104397875  0.169469929  2.673756815  0.405882517
##  [93,] -0.646604416 -0.740495104  0.063231982 -1.095809541 -0.767513218
##  [94,]  1.683330979  1.567742424 -0.698706197  1.431672587 -1.080548515
##  [95,] -1.509921397  0.297490480  0.490010821 -0.323083740 -0.437095352
##  [96,] -0.135237286  0.293266912 -1.015571227 -0.225694168  0.642455326
##  [97,]  0.027644129 -1.133291443 -1.997458759  1.032137750 -0.070625404
##  [98,] -0.637273583 -0.513850978 -0.306967375 -0.684532247  0.140054208
##  [99,]  1.070049729 -2.036508976 -0.316339810 -0.094341352 -0.094161935
## [100,] -0.455435814  0.089328755 -1.403983913 -1.027093674  0.560281943
## [101,]  4.600390311  2.244846920  0.532264308  1.259266636 -1.010942778
## [102,] -0.787145836  1.086091949  0.549806202  1.093912587  0.984179992
## [103,]  0.655142324 -1.683984928 -2.308143986  2.208715115  0.240582243
## [104,] -0.428540034 -0.840500324 -1.048098702 -0.027665882  0.077046929
## [105,] -0.110654721 -0.123171275 -0.175937919  0.338031509  0.196792323
## [106,] -0.734249607 -1.236231879 -1.090037416 -0.386975718 -0.336972535
## [107,]  0.296584193 -0.577728068 -2.014640498  0.588158511  0.632602330
## [108,] -1.410702952  0.429684625 -0.958296105 -0.866024725 -0.101651534
## [109,] -0.418905210 -1.232525386  1.863199813  1.081316900 -0.304585111
## [110,]  0.446752555  1.508585940 -0.342268303 -0.736468382  1.406332814
## [111,] -1.134059417  0.782686222 -0.521004605 -0.152263500 -0.210024740
## [112,]  1.181466882 -2.299898160  0.735344703  0.997333267 -0.237945040
## [113,]  1.830654533  1.883074076  0.954309940  0.626252247  0.685943765
## [114,]  0.454774207 -0.643039459  0.237045213  0.759165544  0.470129822
## [115,]  0.864920996 -1.531113286  1.149483739 -0.984234084 -0.541097522
## [116,] -0.897625868  0.218458064 -0.870977930  0.772271080 -0.128040261
## [117,]  1.357865125 -1.941049776  0.946671254 -0.674767960  0.499517827
## [118,] -0.915336154  1.327339693  0.352068802 -1.370754921 -1.073206670
## [119,]  0.094948933 -0.356826249  1.052712045  0.237447671  0.183785081
## [120,] -0.037442692 -0.108870167 -0.518461408  0.323952099  0.490323176
## [121,] -0.703244230 -0.760629115  0.236405707 -1.666145723 -0.328854978
## [122,]  1.727474232 -1.256161661  0.911292089  0.280268540  0.754418800
## [123,]  1.839479021  0.845697621 -0.141543565  0.392072998 -1.461521820
## [124,]  0.275373090  0.726740366  0.643511448 -0.752337791  0.616212060
## [125,] -0.732974709  1.225314046 -0.703247765  0.876777966  0.813571603
## [126,] -0.921856464  0.796384898 -2.658215899  0.486234753  0.662707828
## [127,] -0.151799435 -0.761905068  1.710990722  1.051731292  0.112226358
## [128,] -1.471716143 -0.654343538 -1.425218658  0.191711126 -0.481284081
## [129,] -1.483838817 -0.227422742  0.005677556  0.103891666 -0.469159558
## [130,] -0.899242135  0.043994478  0.476955011  1.186170494 -0.191676482
## [131,] -1.358439633  0.497908624 -1.167958845  0.193782726  0.263406749
## [132,]  0.549771469 -0.569819028  0.116818203  0.221134190 -0.470229839
## [133,] -1.825714544 -0.294808189  0.619015786 -0.318205481 -0.449230612
## [134,] -1.466418848 -0.825197537  0.473859265  0.509772598 -0.534711905
## [135,]  0.713759778 -0.436347722 -1.423945946  0.210208666 -0.580685346
## [136,]  0.095641779  1.526711941  0.249630093  2.345493852  0.760447203
## [137,] -0.311491252 -0.719233132  0.764263980  0.606336637  0.268751238
## [138,] -0.482193479  0.590787139 -0.436621861 -0.920884510  0.862037778
## [139,]  1.024336162  0.440548826 -0.998470261 -0.555076086 -0.681175727
## [140,]  2.074951928 -0.323134611  1.585536035 -0.925846944 -0.179553069
## [141,] -1.891283328 -0.671701731  0.262065322  0.249157996 -0.686573604
## [142,] -0.768896963 -0.184566117  1.838693762  1.680165112 -0.464801156
## [143,] -0.660225602  1.111821771 -0.488335117  1.229777710  1.056964399
## [144,]  0.458314079  0.872057326 -1.262688367 -0.394557457  1.037856081
## [145,]  0.202499186  0.236773800 -0.635093302  0.249780704  1.069400578
## [146,] -0.635694229 -0.225009929  1.204353392 -1.218165045  0.311045179
## [147,] -1.314850127  0.558262177  1.185628313  0.999319862  0.144248090
## [148,]  2.618727317 -1.043294960 -0.131770830  1.161272958  0.005960761
## [149,] -1.867933212 -0.735989177 -0.971686550 -0.761863164 -0.777526175
## [150,] -0.390204192 -0.137821477  0.220960666 -0.609509106  0.001859155
## [151,] -1.169108179  0.192370763  1.849895119  1.591382674  0.295730175
## [152,] -0.593384345  0.170296655 -0.789961437 -1.081723093  0.289525424
## [153,] -1.153893444  0.470099262 -0.943547532  0.043877107  0.353141392
## [154,] -1.299586961  0.646325766  0.756131408 -0.633505535 -0.632652766
## [155,] -1.312753509  0.646956638 -1.191403488 -0.628395922  0.086051165
## [156,]  2.158951805 -0.669181055  0.329330268 -2.652868558  0.318784824
## [157,] -0.888545794  0.212970263 -0.609333802  1.384522112  0.409559425
## [158,] -1.604599290 -0.895420185  1.536550848  1.466041850 -0.589748801
## [159,] -0.695240701 -1.437349712 -0.294419793  0.105308219 -0.399801541
## [160,]  1.698058938  0.861942358 -2.379230129  0.682957573 -1.045815512
## [161,]  0.523091631  0.622823965 -2.532738018  0.414152379  0.690049934
## [162,] -1.639464234 -0.668476601 -1.067754195  0.831399161 -0.544604009
## [163,] -1.775434759 -0.854401433 -0.150230446 -0.275686146 -0.762810758
## [164,] -1.300191877  0.924773079  0.692943522 -0.083020548  0.311362464
## [165,]  0.127243391  0.547570383 -0.822898988 -0.399221133 -0.079945323
## [166,]  0.728909729 -1.777883731 -1.474530685 -1.729305188  0.173100980
## [167,] -0.691130861  0.504125474 -0.083355531  0.385479113 -0.862138722
## [168,]  4.057107584  0.177251126  2.338537102  0.287960419 -0.658831067
## [169,]  0.065928057 -1.066260062 -0.766093466  0.786318654  0.249756112
## [170,] -1.537449988  0.126535183  1.129984140  0.112397316 -0.018753320
## [171,]  0.005212931  0.571207430 -0.800002711 -1.395337324  0.831843303
## [172,]  1.307010016 -1.130265555 -0.298412422 -1.569287554  0.386355543
## [173,] -1.400091197 -0.281929928  0.503682489  0.734624858 -0.419971994
## [174,] -1.914378275 -0.015175249  0.090929135 -0.639031301 -0.354594968
## [175,] -1.354059138  1.369758171  0.970119313 -0.448346287  0.532923665
## [176,]  1.278137221 -1.653045958  0.582176145  0.663913439  0.681887219
## [177,] -0.240072950  1.468050171 -1.146791696  0.313983803 -0.828208561
## [178,] -1.192542565 -0.620681157  0.393013804  1.386142742 -0.481003615
## [179,]  1.517499402  2.446494185 -0.097915083  0.552779780 -0.177111692
## [180,]  0.419667049 -0.327707583 -0.647757875 -0.752472503 -0.201311865
## [181,] -1.183491054  2.047841110  1.056237863 -0.386605606  1.280456900
## [182,] -0.049231716  0.736575008  0.077583188 -0.705296875  0.945577855
## [183,] -1.497163756 -0.391927377 -2.671606811  0.257351508 -0.356818941
## [184,]  1.362728567  0.566668154 -0.177208297  0.688607859 -1.112237695
## [185,]  3.022520941 -0.826120544  0.734638502 -0.813207184 -0.481935310
## [186,] -0.646848816  0.019961075  0.140097904 -1.345604301  0.174968361
## [187,]  0.841699831 -1.772549530 -0.373832896 -2.173967292 -0.270196135
## [188,] -0.341629561 -0.113562351 -0.165011337 -0.351171147  0.299781146
## [189,]  0.597265999  2.425823378  1.007898127 -0.923443496  0.528966635
## [190,] -1.161264597  0.015537197  0.541717900  1.081599330  0.151672237
## [191,] -0.477014120 -0.313853416 -0.666580443 -0.171072190  0.361420355
## [192,] -2.115125949 -0.729760082  0.102680575 -0.379831150 -0.871667253
## [193,] -0.991130507  1.160119732 -0.454562005 -0.255797516  0.085487828
## [194,] -0.707735717 -1.202340369  0.313311997 -0.079193489 -0.266559479
## [195,]  3.115036491 -0.278203347 -0.068038843  0.730365425 -0.555712164
## [196,] -1.696392904 -0.279442921 -1.520016658 -0.119474656 -0.395871345
## [197,]  0.151090645 -0.052353299 -0.654184084  0.093232715  0.611872104
## [198,]  1.330786502 -1.333832490  1.198984292 -0.592071242 -0.156910522
## [199,]  0.296675856  0.507260694 -0.459773048  0.471858283  1.040250209
## [200,] -0.422623151 -0.772830338  1.475442657  0.229622630 -0.080166317
## [201,] -0.318075869 -0.206265532  0.193138644 -0.150273909  0.272483012
## [202,] -0.085308348  0.324848824 -0.506897761 -0.413457726  0.183316995
## [203,] -1.822877611 -0.578840959 -1.943795566 -0.354374768 -0.657586320
## [204,]  1.201683038  1.016703999 -1.617844139  1.145915109 -0.682858022
## [205,] -1.807181645 -0.673704761 -0.909165251 -0.542600144 -0.697323892
## [206,] -1.784093888 -0.101950630 -1.523967142 -0.547484916 -0.357556116
## [207,] -0.078106596  0.540840034  0.980990841 -0.492489469  1.090629038
## [208,] -0.721328123  0.145142743  1.245670834 -1.005611527  0.493983182
## [209,] -0.483839459 -0.454229646  0.058240719 -0.240884895  0.283251672
## [210,]  0.663630444 -2.030515942  1.095559877 -0.315653418  0.208334029
## [211,]  1.978468906 -1.541564858  0.344229726  0.254916972  0.343867249
## [212,]  2.937647970  0.023153745 -1.467099553  2.004769891 -0.185012738
## [213,] -0.086636710  1.891839624  1.573096232  0.223299508 -2.221106615
## [214,] -1.481813930  0.006331169 -1.173928063 -0.250137785 -0.112924714
## [215,]  0.623006822 -0.037759847 -0.710766534  0.184537311 -0.887891261
## [216,]  1.991882118 -1.666919941 -2.805934883 -0.871488718  0.175942738
## [217,]  0.744165906 -0.860059687 -1.328696095  1.365529752  0.751591017
## [218,]  0.641119818 -0.445632455  0.162013092 -2.055341520  0.923419949
## [219,] -1.586401627 -0.388025617 -1.097489991 -0.453696582 -0.661613141
## [220,]  4.773395918  2.278577670 -1.336404778  0.510730406 -1.718160684
## [221,]  2.921320323 -0.012042086 -1.874368061 -0.045263697 -0.566144677
## [222,]  0.503935335  1.035837075 -1.154051231 -0.866417161  0.131161351
## [223,] -1.241990069  0.411074638  1.790709487  0.707551103  0.092693855
## [224,] -0.133856941 -0.846749537  0.481837944  1.031203316 -0.200664046
## [225,] -1.486223026 -1.226757723  0.663500601  1.212738370 -0.747306389
## [226,] -0.762041381  1.164340422  1.896521625  1.074683686  0.812249845
## [227,]  2.005021660  0.341436716 -0.409217808 -0.832010193  0.147847697
## [228,]  1.814305601  1.684900471  0.545885187 -0.444700098  2.887385706
## [229,] -1.411373860 -0.029800132 -1.219717248 -0.012627251 -0.086502351
## [230,] -0.324175998  0.181346052  0.453617491 -1.500433205 -0.063295422
## [231,] -0.456860329  0.176546846  0.852740264 -0.298237857  0.679884046
## [232,] -1.210396528  0.443593233 -1.157566359 -0.418875718 -1.229168913
## [233,]  0.367888943  1.034558583 -0.899804344 -1.320083756  0.545063435
## [234,] -1.737267642 -0.768492804 -0.717586622 -0.042347936 -0.690091939
## [235,] -1.509987525  0.519084836  0.532663661 -0.793096619 -0.075050898
## [236,] -1.290446225  1.701929130 -0.262965485 -0.898972118  0.974935670
## [237,]  3.655612544  1.679581237 -0.078271387  0.366568656 -1.144046957
## [238,]  0.611276361 -1.193837776  1.025840807 -1.693775105  0.496074659
## [239,]  6.711875034  1.215508748 -1.279625142  0.587766000 -0.938041730
## [240,] -1.281390399 -0.456797389  0.383696463  1.327109609 -0.434647734
## [241,]  0.776720455  0.873249312 -0.255587193  0.950034593  1.789939090
## [242,]  0.008347450  1.173046306  1.625650682 -0.126758712  1.284764016
## [243,] -0.958826089 -0.492058288  0.745646701 -1.985299776 -0.313503201
## [244,]  1.609087788  0.768291741  1.106856868  1.288165361 -1.317902920
## [245,]  0.543831815 -0.344117364  1.084227436  0.743018250 -0.049164466
## [246,] -1.795501728  0.797766300  0.941073658 -0.948765046  0.188093947
## [247,] -2.078996209  0.034041364  0.343126833 -1.053156920 -0.428421322
## [248,]  0.486998129  0.122844418 -0.822868404  1.350720580  0.697385548
## [249,] -0.821657492 -0.011924402  0.873543779  1.971662603  0.110811955
## [250,] -1.398504155 -0.243599402  0.837410828  0.477686433 -0.150887846
## [251,]  0.526594325 -1.361027292  1.730491888  0.644317870 -0.904698848
## [252,]  0.120809384 -1.392425032 -0.882175385  0.251835439  0.060510736
## [253,] -0.289560811 -1.753881720  0.731478923  1.008115634 -0.564319747
## [254,]  2.350354264 -1.374432502  0.783487702  1.516771930  0.201694966
## [255,]  2.529945185 -0.796264796 -1.084229732 -1.768591624  1.468016449
## [256,] -0.594294620  0.606268901  0.546284310 -1.512570945  0.547901821
## [257,] -1.406577585  0.312852106 -0.020482861  0.091002001 -0.110026066
## [258,] -1.651971076 -0.143369845 -1.143133022 -0.250064542 -0.291778062
## [259,]  0.415871178 -0.214174686  0.915948123  0.956618386  0.974131542
## [260,] -0.286827613 -0.440600376 -0.511227621 -0.188717119  0.390008978
## [261,] -0.645411407  0.058506107 -2.305257330  2.581332331  0.223956712
## [262,] -0.628353063 -1.040695063  1.499765220  0.328717274 -0.091370940
## [263,] -0.136446586 -0.912547265  0.240795333  0.609862680 -0.011841605
## [264,] -1.777655604 -0.274014123 -1.028075306 -0.764011769 -0.961634321
## [265,] -1.357302997  2.288698502  1.019344070 -1.133889152  1.295074700
## [266,] -1.150407815 -1.178196185  0.453312973 -1.488628969 -0.550910191
## [267,] -0.854919366  2.319121839 -0.534036982 -0.401249649  1.590398378
## [268,]  1.748954057 -2.489466264  0.147763981  1.527744484 -0.031497689
## [269,] -0.738423976 -0.871268532 -1.716222096 -0.549433967 -0.141152979
## [270,] -0.346935263  1.923554748 -1.292856361 -0.360145431 -0.649527552
## [271,]  2.611945346 -0.868543943 -0.456914061  1.833405222 -0.121158473
## [272,] -0.054669716  0.467014101 -0.459580646  0.187565076  0.815668207
## [273,]  0.590763284  0.081986670 -0.821826225  1.066920091  0.715892272
## [274,] -0.771766282  0.497567733 -0.144543170 -0.043136586 -1.433593942
## [275,]  0.287407340 -0.999343796 -0.141647094  1.726767706  0.460339894
## [276,] -1.904210848 -0.711924915 -0.636156799  0.229311959 -0.732363166
## [277,]  1.980934953 -2.144737237 -1.558960290 -1.734660915  0.372677052
## [278,]  4.349982486  0.818990696 -1.850629065  0.156456507 -0.310120302
## [279,] -1.601460087  0.466219801  0.555412046 -1.282120597 -0.177034377
## [280,]  1.110817200 -0.894199685  0.626718163 -1.090577512  0.457144316
## [281,] -1.635586546  0.585764692  0.351472824 -0.436299965  0.162468184
## [282,] -0.910449829 -0.063109780 -0.243265787  1.440217859 -0.008738371
## [283,]  0.979721615  0.904442368 -1.232199254  1.008144535 -0.363957491
## [284,] -0.472435837 -0.521473629  0.942802823  0.140237047  0.029009438
## [285,]  0.298128461 -0.439838094 -0.230211394  0.045875504  0.466431500
## [286,]  0.876478490 -0.632485240 -2.150246922  0.523252544 -0.354676442
## [287,]  0.030556752 -0.246001099 -1.050954176 -0.130320899  0.416685941
## [288,]  0.489276289  0.149716001  1.343990756 -0.776952747 -1.363924275
## [289,]  1.167193218  4.324487587  0.744165112 -1.104452819 -2.960549114
## [290,]  5.639123713  1.493129585  0.436631086  0.391589194  1.328124017
## [291,]  0.076038156  2.149080398  1.231684279 -0.889701456  2.108001645
## [292,] -1.306362503  0.777428880 -0.836033189 -0.505010722  0.429704777
## [293,] -1.492629535  0.346667458 -1.594060891 -0.744201427  0.053005921
## [294,]  0.548191410  0.159332266  1.521957843  0.691090269  0.002822644
## [295,]  3.173294742 -0.713640891  1.483201289 -0.597042450 -0.955008287
## [296,] -1.711510331  0.207909220 -0.931632873 -0.732023246 -0.134887380
## [297,] -1.420928885 -1.297938310  0.314667960  1.070874265 -0.766364136
## [298,] -0.397038374 -0.140558009 -0.100049951 -1.210608408 -0.287822450
## [299,] -1.338159554  0.850035604  0.991498508  0.275292019  0.519975147
## [300,]  1.238726422 -0.682019739 -1.206227105 -1.584533216  0.599257188
## [301,]  0.476798036 -0.538294379  1.306977504  0.589987890  0.804993508
## [302,]  0.451358041  0.509847268 -0.404959275  1.025191596  1.150524367
## [303,] -0.410664267  1.809811675  0.163254213  1.203959868  1.107465182
## [304,]  0.631511135  4.553878477  0.617849698 -0.258625983  0.452803511
## [305,]  0.606275351  1.307303704 -1.190130416 -1.085147986  0.839582865
## [306,]  3.760469200 -1.318016453 -1.571659239 -0.958198521 -0.168654341
## [307,]  0.283257978  0.334225557  0.900109850  1.387190281  0.742119351
## [308,]  1.205872572 -1.025116718 -0.694241491 -0.489820821  0.185091372
## [309,] -0.547890175 -1.378267017  0.199506501  0.006777245 -0.282776412
## [310,]  0.675442079 -0.040092847  0.040280714  1.538300103  0.724233244
## [311,] -0.347420655 -1.297275709 -0.084885546  0.216594996 -0.374740492
## [312,] -1.082694803  1.058501944 -1.274637266 -0.535652316 -0.301170989
## [313,] -0.809911038  0.678119879 -0.193503870  0.489931605 -0.567989774
## [314,]  2.814192996  1.465015414  1.296910650 -1.024401483 -0.754090861
## [315,] -1.219216145 -0.216402526  0.775638956  0.706433637 -0.029531003
## [316,] -0.839858529 -1.160921154 -0.067522123 -0.376613864 -0.332337533
## [317,]  1.906604890 -1.476681383 -0.028831221  0.037013607  1.083914038
## [318,] -1.128786006  0.395890021  0.040446729  0.390323605 -0.149885563
## [319,]  4.980287452  1.400993226  0.386980437  0.646687478 -1.083846603
## [320,] -0.396555408 -0.215395452 -1.222389233 -0.813225124  0.424557329
## [321,] -1.686147468  0.664222126  1.210799613 -0.375476795  0.198108774
## [322,] -0.771587552  0.001912498 -0.021523533  2.182231316  0.393142757
## [323,]  2.121003409 -2.080663494  0.161998088  0.897550000  0.380306029
## [324,]  0.183525269  0.711131176  0.676974276 -0.837925098 -0.201495035
## [325,] -0.388480855 -0.019183155 -0.034180507 -0.379134234  0.583222451
## [326,] -0.270374270  0.372642009  0.619830911 -1.148519958 -0.407017698
## [327,] -0.016309255 -0.272150173  1.123754077 -0.347941297 -0.103237180
## [328,] -1.509365115 -1.227221931  0.110956778  1.437386493 -0.758506439
## [329,]  1.128006246 -1.746278013  0.499382396 -1.619420542  0.555724903
## [330,] -0.013678857  0.097843119  0.408072714 -0.795855347 -1.175223096
## [331,]  0.134239505  0.261168839  1.687827776  0.217195174  1.082628063
## [332,]  0.543266130  0.289044087 -1.889627887  1.415180585  1.063577278
## [333,] -1.694510184 -0.384164773  0.978956440 -0.619188118 -0.943767153
## [334,] -1.177192240  0.755347480 -0.072837954  0.262273753  0.532730202
## [335,] -0.154704801 -0.482019591 -0.130393501  0.108703255  0.455787032
## [336,] -1.222393212 -0.140605864  0.470903440  0.854635087 -0.236602493
## [337,]  0.985284375 -2.085350193 -0.309169317 -0.356636930  0.209646403
## [338,]  1.845084419 -1.284127961 -0.428328294 -1.460289251  0.838247554
## [339,] -1.537001279  1.111570387  0.652894920 -1.060718845 -0.002140100
## [340,]  0.486580696 -0.438599188 -0.143918334  0.966749788  0.107166844
## [341,] -0.381846642 -0.365594889  0.626052636  0.039508221 -0.092159877
## [342,] -1.058469609  1.839970213 -0.254329772 -0.731552164 -0.827823834
## [343,]  1.953784231 -1.229071105  0.160259672  0.867246394  1.295990204
## [344,] -1.632770525 -0.310017947  0.586575867  0.624972262 -0.312659105
## [345,] -0.069211481  1.179578849 -0.019456868 -1.025693279  0.424192027
## [346,]  0.924645953  0.318200997 -0.038558980 -0.176342543 -1.278270521
## [347,] -1.679627649 -0.870249748  1.201962925  0.638583744 -0.657934688
## [348,] -0.138978457 -0.327879510  1.445999742  0.018109114  0.324021275
## [349,] -0.306354427  2.443421548  0.256738595  0.723881262  0.004780055
## [350,] -1.082397105  0.511694553  0.396630701  0.376171916  0.200267508
## [351,]  1.560087096 -0.172608049  2.042673531  0.001387343  0.943307040
## [352,]  0.213890453  0.121650120 -0.363220480  0.143134581  0.251009799
## [353,] -1.243101129 -0.469575151 -1.404226113  1.148855158 -0.206147146
## [354,] -1.723673624 -0.628891973  1.215101216  0.822337346 -0.530509884
## [355,] -1.845736715 -1.246640827  1.218806001  0.592440275 -0.970712299
## [356,] -0.533908899  0.509703545 -1.010222476 -1.067833304  0.770760459
## [357,] -0.621852817  1.060330174 -0.185420284  0.974853637  0.788314716
## [358,] -0.663822556 -0.698693563 -1.437208451 -1.000964685 -0.267520648
## [359,] -1.464448793 -0.997923794  0.090438438  0.991886193 -0.619748924
## [360,] -1.523194528  1.088366756 -0.015584201 -1.071387626  0.484479318
## [361,] -0.249284791 -0.495162923 -0.888175969  0.194375075  0.137323234
## [362,] -0.978278825  0.745196276  1.673492426  0.624652999  0.677279063
## [363,]  2.298810986 -0.090143085 -0.751106742 -0.561856912  1.569191798
## [364,] -0.641761160 -1.573225212  0.960424847 -0.179437036 -0.696431558
## [365,] -1.237501132 -0.412442737  1.793811573  1.137104529 -0.371283677
## [366,] -1.157403928  0.923508573 -0.442026074 -0.884941552 -0.171459484
## [367,] -0.796933393  1.222876039  0.723404723 -0.237384378 -0.510118334
## [368,]  2.646899548  0.301553970  0.690593527 -2.443750630  0.663805037
## [369,] -0.178975454 -0.138624086  1.105283992 -1.499072183 -0.164055484
## [370,] -1.330874437  0.769296425 -0.127097036 -1.223980155 -0.869663470
## [371,]  0.785519987  2.132318925  0.981263612 -0.639682484 -0.035075161
## [372,]  4.528600634 -0.995996130  0.568209680 -0.292649916 -0.397415282
## [373,] -2.215387412 -0.717213408  0.437807288 -1.098624561 -0.945243579
## [374,]  0.852816653  0.697424945 -0.415247520  0.859928559  0.964247801
## [375,]  1.528575274  1.579100810  0.424898608  1.740887715 -0.368739736
## [376,]  1.052831636  0.469776583  0.746395631 -0.477473960 -1.373515237
## [377,]  3.308075529 -0.637217047 -0.361014725 -0.281269186 -0.462933899
## [378,]  0.145308323 -0.337470348  1.183817291  1.285154406  0.271835930
## [379,] -0.100434292 -0.148112235  0.886936726  0.259148546  0.704812541
##                 PC6
##   [1,]  0.116709537
##   [2,]  0.110173000
##   [3,]  0.151011377
##   [4,] -0.343807479
##   [5,] -0.068417317
##   [6,] -0.420280958
##   [7,]  0.014839886
##   [8,]  0.336718257
##   [9,] -0.045952454
##  [10,]  1.939826284
##  [11,] -0.146897222
##  [12,]  0.183314250
##  [13,]  0.114162471
##  [14,] -0.102727402
##  [15,]  0.196911289
##  [16,] -0.296960713
##  [17,] -0.346683316
##  [18,]  0.385229903
##  [19,]  0.250212417
##  [20,]  0.210997273
##  [21,]  0.178758339
##  [22,] -0.003801151
##  [23,]  0.217319459
##  [24,] -0.187966712
##  [25,] -0.249408299
##  [26,]  0.582504343
##  [27,] -0.264956027
##  [28,] -0.324073726
##  [29,]  0.392690074
##  [30,]  0.433561922
##  [31,] -0.044052794
##  [32,] -0.172924722
##  [33,] -0.273046392
##  [34,] -0.339264995
##  [35,]  0.377235819
##  [36,] -0.090271827
##  [37,]  0.414287669
##  [38,] -0.393701821
##  [39,]  0.033505637
##  [40,]  0.354862667
##  [41,]  0.077217544
##  [42,] -0.251343699
##  [43,]  0.437209594
##  [44,]  0.418033744
##  [45,]  0.092143326
##  [46,]  0.453442755
##  [47,]  0.025217332
##  [48,] -0.198309910
##  [49,]  0.187074835
##  [50,]  0.063584865
##  [51,]  0.411945392
##  [52,]  0.347020693
##  [53,] -1.602200768
##  [54,] -0.297652746
##  [55,]  0.140534670
##  [56,] -0.120117267
##  [57,]  0.295188323
##  [58,] -0.436240290
##  [59,] -0.241532009
##  [60,] -0.152644965
##  [61,] -0.340782009
##  [62,] -0.237639469
##  [63,]  0.300926071
##  [64,] -0.253457399
##  [65,] -0.123036265
##  [66,] -0.318934216
##  [67,]  0.157579795
##  [68,] -0.260813996
##  [69,] -0.245354609
##  [70,] -0.305254302
##  [71,] -1.882250425
##  [72,]  0.409598000
##  [73,]  0.232202465
##  [74,] -0.149057573
##  [75,]  0.545903188
##  [76,]  0.277588617
##  [77,]  0.361912198
##  [78,] -0.478016137
##  [79,] -0.412381253
##  [80,] -0.183130748
##  [81,]  0.233456245
##  [82,] -0.356154388
##  [83,]  0.449569521
##  [84,] -0.185788498
##  [85,] -0.219609958
##  [86,] -0.001711114
##  [87,] -1.559617792
##  [88,] -0.428893296
##  [89,] -0.349853393
##  [90,]  0.067731920
##  [91,]  0.142796842
##  [92,] -0.180830638
##  [93,]  0.315292384
##  [94,]  0.557663845
##  [95,] -0.172373827
##  [96,]  0.407727459
##  [97,]  0.327538602
##  [98,]  0.346056104
##  [99,]  2.163269668
## [100,]  0.345529449
## [101,]  0.138719045
## [102,] -0.279523523
## [103,] -0.084975054
## [104,]  0.337408982
## [105,]  0.436700603
## [106,]  0.388716289
## [107,]  0.023800405
## [108,] -0.344894615
## [109,]  0.380430817
## [110,]  0.059212100
## [111,] -0.160062648
## [112,]  0.451808896
## [113,] -0.328134576
## [114,] -0.232509061
## [115,]  0.417691744
## [116,] -0.283499777
## [117,] -0.334241319
## [118,] -0.354492127
## [119,]  0.016626218
## [120,]  0.329368287
## [121,]  0.014802916
## [122,]  1.788209994
## [123,] -0.225290106
## [124,] -0.049381001
## [125,] -0.176037238
## [126,] -0.147416810
## [127,]  0.274931744
## [128,] -0.288402296
## [129,] -0.238830171
## [130,] -0.321394130
## [131,] -0.060804904
## [132,] -0.198430755
## [133,] -0.201882037
## [134,] -0.416230299
## [135,] -0.104823016
## [136,] -0.259292999
## [137,]  0.309515655
## [138,]  0.473433423
## [139,] -0.224455247
## [140,] -0.113549634
## [141,] -0.029270791
## [142,] -0.408139727
## [143,] -0.249679273
## [144,]  0.052432954
## [145,]  0.123609326
## [146,]  0.110721474
## [147,]  0.039482206
## [148,] -0.055563924
## [149,] -0.301541438
## [150,]  0.339761189
## [151,] -0.143565175
## [152,]  0.495882321
## [153,] -0.338275303
## [154,] -0.259013852
## [155,] -0.268105530
## [156,] -0.980893416
## [157,] -0.246803124
## [158,] -0.078306763
## [159,]  0.382030122
## [160,]  0.087323777
## [161,]  0.376505108
## [162,]  0.053401289
## [163,] -0.338300621
## [164,] -0.183747770
## [165,]  0.432642111
## [166,]  0.187719391
## [167,] -0.323645603
## [168,]  0.829006715
## [169,]  0.043491740
## [170,] -0.248046133
## [171,] -0.060255793
## [172,] -0.083545793
## [173,] -0.167508321
## [174,] -0.089468938
## [175,] -0.143831223
## [176,]  0.323860642
## [177,] -0.174432941
## [178,] -0.239734115
## [179,]  0.497289814
## [180,] -0.327540210
## [181,] -0.151688764
## [182,]  0.197182238
## [183,] -0.042715485
## [184,]  0.044010655
## [185,] -0.925270972
## [186,]  0.322942444
## [187,] -0.036587651
## [188,]  0.356359819
## [189,]  0.423139332
## [190,] -0.257850948
## [191,]  0.463686146
## [192,] -0.032295644
## [193,] -0.221120598
## [194,]  0.347410914
## [195,] -0.102882758
## [196,] -0.052886406
## [197,]  0.099771649
## [198,]  0.161046943
## [199,]  0.245795874
## [200,]  0.272924190
## [201,]  0.339839246
## [202,]  0.395294558
## [203,] -0.065386536
## [204,]  0.561844444
## [205,] -0.271407182
## [206,] -0.059059407
## [207,]  0.083045883
## [208,]  0.377344777
## [209,]  0.334594979
## [210,]  2.210117773
## [211,] -0.225352991
## [212,]  0.659498155
## [213,]  0.005821771
## [214,] -0.246898562
## [215,]  0.168733702
## [216,] -0.366893261
## [217,] -0.293117425
## [218,]  0.423293245
## [219,] -0.277523269
## [220,]  0.108760866
## [221,]  0.070710680
## [222,]  0.163384108
## [223,] -0.232906221
## [224,]  0.408184032
## [225,] -0.300209061
## [226,] -0.343281023
## [227,]  0.380266460
## [228,]  0.475769439
## [229,] -0.240418547
## [230,]  0.118544474
## [231,]  0.411577815
## [232,] -0.017746096
## [233,] -0.022662183
## [234,] -0.215224961
## [235,] -0.336453644
## [236,] -0.208327609
## [237,]  0.415886191
## [238,]  0.260849310
## [239,] -0.336942900
## [240,] -0.122484819
## [241,] -0.025660118
## [242,]  0.330693931
## [243,]  0.187450418
## [244,]  0.092254142
## [245,] -0.103389100
## [246,] -0.135338511
## [247,] -0.081072198
## [248,]  0.345962874
## [249,] -0.250967381
## [250,] -0.344899324
## [251,] -0.429960219
## [252,] -0.282830186
## [253,]  0.174435063
## [254,] -0.002994835
## [255,] -1.217412358
## [256,]  0.360421127
## [257,] -0.146287428
## [258,] -0.133025274
## [259,] -0.126146676
## [260,]  0.220778323
## [261,]  0.108029807
## [262,]  0.349752615
## [263,]  0.200005121
## [264,] -0.101933578
## [265,] -0.161334026
## [266,]  0.285586865
## [267,] -0.238563544
## [268,]  0.083679922
## [269,]  0.509906873
## [270,] -0.146139621
## [271,]  0.334416111
## [272,]  0.473647831
## [273,]  0.136442835
## [274,] -0.251405937
## [275,]  0.114366181
## [276,]  0.048022334
## [277,] -1.054946234
## [278,] -0.700681151
## [279,] -0.434292485
## [280,]  0.255500421
## [281,] -0.124820953
## [282,] -0.258508925
## [283,]  0.519297048
## [284,]  0.418680932
## [285,] -0.218443452
## [286,] -0.216123751
## [287,]  0.115923969
## [288,] -0.027866918
## [289,] -0.058716464
## [290,] -2.000384525
## [291,]  0.277974900
## [292,] -0.293421787
## [293,] -0.259635342
## [294,]  0.059625913
## [295,]  0.971487465
## [296,] -0.150615259
## [297,] -0.400937784
## [298,]  0.238954410
## [299,] -0.144937084
## [300,]  0.201952185
## [301,] -0.447834040
## [302,]  0.281901496
## [303,] -0.203869133
## [304,] -0.134202490
## [305,] -0.059036104
## [306,] -1.689975498
## [307,]  0.458648969
## [308,]  0.521154125
## [309,]  0.178933466
## [310,]  0.097184547
## [311,]  0.178727506
## [312,] -0.114849810
## [313,] -0.177928676
## [314,]  0.278091472
## [315,] -0.424718686
## [316,]  0.421376781
## [317,] -0.381796482
## [318,] -0.221941061
## [319,] -0.754255469
## [320,]  0.249838558
## [321,] -0.111526776
## [322,] -0.207650126
## [323,] -0.362767449
## [324,]  0.207891984
## [325,]  0.340268457
## [326,]  0.368766457
## [327,]  0.012058601
## [328,] -0.149559490
## [329,]  1.463155184
## [330,]  0.382942476
## [331,] -0.032112095
## [332,]  0.397084457
## [333,] -0.354911460
## [334,] -0.233823936
## [335,]  0.146812456
## [336,] -0.250028422
## [337,]  0.205107833
## [338,] -0.667916271
## [339,] -0.159417162
## [340,]  0.044940196
## [341,]  0.444365443
## [342,]  0.218371896
## [343,] -0.083864131
## [344,] -0.066718642
## [345,]  0.460637350
## [346,]  0.010040209
## [347,] -0.249703684
## [348,]  0.069849151
## [349,]  0.133553509
## [350,] -0.337335972
## [351,]  0.358285729
## [352,]  0.221064477
## [353,] -0.125296735
## [354,] -0.070458295
## [355,] -0.224997131
## [356,]  0.501370980
## [357,] -0.349367892
## [358,]  0.380452253
## [359,] -0.271394600
## [360,] -0.258419685
## [361,]  0.402658885
## [362,] -0.468027915
## [363,] -0.324990632
## [364,]  0.142034987
## [365,] -0.347928412
## [366,] -0.351391164
## [367,] -0.285977778
## [368,] -0.971457197
## [369,] -0.181523245
## [370,] -0.240725882
## [371,]  0.387573331
## [372,] -0.229079837
## [373,] -0.209054420
## [374,]  0.036780440
## [375,]  0.503922523
## [376,] -0.173505314
## [377,] -0.787406645
## [378,]  0.319960047
## [379,]  0.154968029
plot(Cancer_pca)

#get the original value of the data based on PCA
center <- Cancer_pca$center
scale <- Cancer_pca$scale
new_Cancer <- as.matrix(Cancer[,-1])
new_Cancer
##        Age Stage Tumor Size Regional Node Examined Reginol Node Positive
##   [1,]  68     1          4                     24                     1
##   [2,]  50     2         35                     14                     5
##   [3,]  58     3         63                     14                     7
##   [4,]  58     1         18                      2                     1
##   [5,]  47     2         41                      3                     1
##   [6,]  51     1         20                     18                     2
##   [7,]  51     1          8                     11                     1
##   [8,]  40     2         30                      9                     1
##   [9,]  40     4        103                     20                    18
##  [10,]  69     4         32                     21                    12
##  [11,]  68     1         13                      9                     1
##  [12,]  46     3         59                     11                     3
##  [13,]  65     2         35                     13                     3
##  [14,]  48     1         15                     23                     7
##  [15,]  62     2         35                     16                    14
##  [16,]  61     1         19                     20                     1
##  [17,]  56     2         46                      1                     1
##  [18,]  43     2         24                     22                     1
##  [19,]  48     2         25                     16                     1
##  [20,]  60     2         29                     20                     1
##  [21,]  48     2         30                     15                     2
##  [22,]  57     2         40                     15                     5
##  [23,]  55     2         29                      4                     1
##  [24,]  48     3         70                     18                     1
##  [25,]  62     1         20                     26                    22
##  [26,]  63     2         22                     31                    17
##  [27,]  48     2         50                     25                    23
##  [28,]  46     1         17                     14                     1
##  [29,]  57     2         25                     14                     4
##  [30,]  66     2         21                     10                     1
##  [31,]  47     2         40                      3                     1
##  [32,]  53     1         15                      5                     1
##  [33,]  59     1         15                      6                     1
##  [34,]  60     1         20                     19                     3
##  [35,]  46     2         30                     19                    10
##  [36,]  51     1         10                      9                     2
##  [37,]  54     2         27                     21                     6
##  [38,]  51     1         18                     14                     2
##  [39,]  49     2         35                     10                     2
##  [40,]  51     2         23                     15                     5
##  [41,]  57     3         70                     12                    12
##  [42,]  64     1         17                     12                     2
##  [43,]  62     2         21                      2                     1
##  [44,]  53     2         23                     15                     6
##  [45,]  55     1          5                     11                     2
##  [46,]  66     3         51                     10                     5
##  [47,]  42     1          9                     15                     2
##  [48,]  62     1         15                     12                     1
##  [49,]  53     2         32                     16                     9
##  [50,]  69     1          5                      8                     3
##  [51,]  37     2         23                     17                     3
##  [52,]  69     3         55                      9                     1
##  [53,]  60     3        120                      7                     1
##  [54,]  63     3         77                     20                     2
##  [55,]  57     1          2                     16                     1
##  [56,]  55     1         11                     13                     1
##  [57,]  62     2         25                     19                     1
##  [58,]  50     1         18                     49                     1
##  [59,]  50     1         15                     15                     1
##  [60,]  55     1         12                     17                     2
##  [61,]  56     1         18                     24                     2
##  [62,]  51     1         17                     12                     1
##  [63,]  42     2         26                      1                     1
##  [64,]  59     3         75                     20                     2
##  [65,]  67     1         13                     16                     3
##  [66,]  46     1         15                      5                     1
##  [67,]  31     3         70                     23                    23
##  [68,]  40     1         15                     20                     3
##  [69,]  58     1         15                      5                     1
##  [70,]  52     1         17                     12                     3
##  [71,]  49     3        130                     12                     8
##  [72,]  64     2         34                     24                    20
##  [73,]  31     2         30                     16                     1
##  [74,]  66     1         10                     15                     1
##  [75,]  67     2         22                     19                    16
##  [76,]  56     3         55                     13                     1
##  [77,]  66     2         25                     11                     4
##  [78,]  42     2         50                      7                     1
##  [79,]  51     2         50                      9                     1
##  [80,]  68     1         15                      9                     1
##  [81,]  53     2         30                     21                    13
##  [82,]  67     1         20                     10                     1
##  [83,]  66     2         22                      9                     2
##  [84,]  53     1         15                      2                     1
##  [85,]  51     1         15                     13                     1
##  [86,]  46     2         40                     12                    11
##  [87,]  48     3        120                      7                     5
##  [88,]  52     3         80                     10                     1
##  [89,]  55     1         17                     11                     1
##  [90,]  65     1          3                      9                     1
##  [91,]  53     3         60                      8                     1
##  [92,]  33     1         14                     15                     1
##  [93,]  63     2         26                      5                     4
##  [94,]  45     2         25                     21                    16
##  [95,]  59     1         12                     12                     3
##  [96,]  60     2         25                     17                     2
##  [97,]  50     2         30                      4                     2
##  [98,]  61     2         25                     10                     1
##  [99,]  50     4         24                      3                     3
## [100,]  68     2         27                     14                     1
## [101,]  38     3         70                     33                    24
## [102,]  47     1         16                     25                     1
## [103,]  39     2         45                      3                     1
## [104,]  57     2         27                      7                     1
## [105,]  52     2         23                     14                     3
## [106,]  60     2         25                      2                     1
## [107,]  54     2         40                     11                     1
## [108,]  68     1         20                     12                     2
## [109,]  38     2         21                      8                     2
## [110,]  63     2         36                     30                     3
## [111,]  61     1         14                     15                     4
## [112,]  37     3         51                      3                     3
## [113,]  46     2         50                     34                    10
## [114,]  45     2         45                     14                     2
## [115,]  54     3         51                      6                     5
## [116,]  53     1         19                     12                     3
## [117,]  50     3         76                      9                     1
## [118,]  69     1         20                     16                     9
## [119,]  48     2         35                     15                     3
## [120,]  53     2         27                     15                     2
## [121,]  67     2         35                      7                     2
## [122,]  43     4         35                     15                     3
## [123,]  50     2         50                     16                    16
## [124,]  59     2         38                     23                     4
## [125,]  53     1         15                     23                     2
## [126,]  62     1         17                     16                     1
## [127,]  39     2         25                     13                     2
## [128,]  59     1         19                      3                     1
## [129,]  56     1         15                      8                     2
## [130,]  45     1         18                     13                     3
## [131,]  60     1         11                     14                     1
## [132,]  50     2         45                     10                     6
## [133,]  58     1         12                      8                     1
## [134,]  50     1         20                      5                     1
## [135,]  55     2         45                      8                     7
## [136,]  37     1         18                     28                     5
## [137,]  46     2         25                     12                     1
## [138,]  65     2         21                     20                     1
## [139,]  61     2         49                     14                    10
## [140,]  52     3         70                     18                     9
## [141,]  54     1          7                      4                     1
## [142,]  36     1         19                     13                     4
## [143,]  49     1         17                     24                     1
## [144,]  62     2         38                     23                     3
## [145,]  54     2         34                     20                     1
## [146,]  61     2         30                     15                     1
## [147,]  46     1          4                     18                     2
## [148,]  38     3         72                     13                     8
## [149,]  66     1         18                      1                     1
## [150,]  59     2         25                     13                     3
## [151,]  38     1          9                     18                     1
## [152,]  67     2         21                     14                     2
## [153,]  60     1         20                     15                     1
## [154,]  61     1         15                     14                     5
## [155,]  67     1         18                     14                     2
## [156,]  69     3        100                     16                     6
## [157,]  47     1         17                     15                     1
## [158,]  39     1          7                      6                     1
## [159,]  53     2         24                      2                     1
## [160,]  55     2         43                     14                    14
## [161,]  59     2         30                     18                     4
## [162,]  53     1          7                      3                     1
## [163,]  59     1         18                      2                     1
## [164,]  57     1         12                     20                     2
## [165,]  61     2         25                     16                     6
## [166,]  68     3         62                      3                     1
## [167,]  54     1         20                     12                     7
## [168,]  37     4         70                     24                    17
## [169,]  48     2         37                      8                     1
## [170,]  53     1         13                     14                     1
## [171,]  69     2         40                     20                     2
## [172,]  63     3         70                     11                     3
## [173,]  49     1         12                      9                     2
## [174,]  63     1          9                      9                     1
## [175,]  60     1         10                     24                     2
## [176,]  41     3         55                     11                     1
## [177,]  59     1         18                     17                    10
## [178,]  43     1         15                      7                     2
## [179,]  52     2         25                     31                    14
## [180,]  61     2         50                     11                     5
## [181,]  60     1         10                     32                     1
## [182,]  61     2         30                     23                     2
## [183,]  63     1         13                      3                     1
## [184,]  48     2         40                     15                    13
## [185,]  51     3        100                     14                    11
## [186,]  66     2         25                     14                     2
## [187,]  68     3         68                      3                     3
## [188,]  58     2         25                     14                     2
## [189,]  62     2         23                     34                     9
## [190,]  46     1         15                     14                     1
## [191,]  58     2         22                     12                     1
## [192,]  60     1          7                      2                     1
## [193,]  62     1         16                     19                     4
## [194,]  53     2         24                      5                     1
## [195,]  42     3         75                     16                    13
## [196,]  63     1         11                      5                     1
## [197,]  55     2         35                     16                     2
## [198,]  50     3         60                     10                     5
## [199,]  52     2         30                     22                     2
## [200,]  47     2         25                     11                     2
## [201,]  55     2         25                     14                     2
## [202,]  60     2         25                     16                     4
## [203,]  66     1         12                      1                     1
## [204,]  50     2         25                     17                    12
## [205,]  64     1         17                      2                     1
## [206,]  67     1         11                      6                     1
## [207,]  56     2         32                     24                     1
## [208,]  60     2         21                     18                     1
## [209,]  56     2         25                     12                     1
## [210,]  48     4         19                      6                     1
## [211,]  44     3         75                     11                     4
## [212,]  37     3         52                     17                    12
## [213,]  52     1          9                     18                    17
## [214,]  63     1         17                      9                     1
## [215,]  54     2         35                     10                     9
## [216,]  63     3         85                      4                     4
## [217,]  44     2         50                     12                     1
## [218,]  68     3         51                     17                     1
## [219,]  64     1         18                      4                     2
## [220,]  50     3         75                     27                    27
## [221,]  55     3         72                     14                    13
## [222,]  66     2         35                     20                     7
## [223,]  46     1         12                     18                     2
## [224,]  43     2         23                      9                     3
## [225,]  43     1         16                      2                     1
## [226,]  43     1         16                     27                     2
## [227,]  59     3         57                     20                     9
## [228,]  55     3         50                     42                     1
## [229,]  61     1         17                      9                     1
## [230,]  66     2         32                     15                     4
## [231,]  55     2         21                     19                     1
## [232,]  65     1         11                      7                     7
## [233,]  69     2         40                     22                     5
## [234,]  59     1         15                      2                     1
## [235,]  63     1         17                     15                     2
## [236,]  68     1         14                     26                     1
## [237,]  48     3         60                     26                    21
## [238,]  61     3         55                     12                     1
## [239,]  43     4        120                     28                    26
## [240,]  44     1         11                      8                     2
## [241,]  47     2         39                     29                     1
## [242,]  52     2         23                     30                     2
## [243,]  69     2         28                      9                     2
## [244,]  39     2         37                     18                    15
## [245,]  43     2         40                     15                     5
## [246,]  64     1          9                     18                     1
## [247,]  66     1          8                      9                     1
## [248,]  45     2         28                     18                     3
## [249,]  37     1         15                     15                     2
## [250,]  50     1         17                     11                     1
## [251,]  40     2         50                      6                     6
## [252,]  52     2         48                      5                     1
## [253,]  41     2         30                      2                     2
## [254,]  32     3         68                     13                     6
## [255,]  65     3        110                     19                     2
## [256,]  67     2         23                     20                     2
## [257,]  57     1         12                     13                     2
## [258,]  63     1         13                      7                     1
## [259,]  42     2         40                     20                     1
## [260,]  57     2         30                     12                     1
## [261,]  42     1          9                     11                     2
## [262,]  46     2         22                      9                     1
## [263,]  47     2         30                      9                     2
## [264,]  67     1         12                      3                     3
## [265,]  67     1         10                     33                     1
## [266,]  65     2         25                      3                     1
## [267,]  65     1         16                     33                     1
## [268,]  33     3         65                      3                     3
## [269,]  64     2         22                      4                     1
## [270,]  66     1         17                     20                    10
## [271,]  34     3         60                     13                     9
## [272,]  55     2         22                     20                     2
## [273,]  47     2         35                     18                     3
## [274,]  58     1         18                      9                     9
## [275,]  38     2         34                     11                     1
## [276,]  57     1          6                      2                     1
## [277,]  65     3        105                      4                     2
## [278,]  52     3        100                     23                    17
## [279,]  67     1         20                     14                     2
## [280,]  57     3         57                     14                     3
## [281,]  61     1         10                     16                     1
## [282,]  45     1         17                     12                     2
## [283,]  50     2         25                     18                    10
## [284,]  50     2         21                     12                     2
## [285,]  53     2         45                     14                     2
## [286,]  54     2         50                      7                     6
## [287,]  58     2         35                     13                     2
## [288,]  56     2         38                     12                    11
## [289,]  68     1         16                     30                    28
## [290,]  41     3        140                     41                    15
## [291,]  61     2         25                     39                     1
## [292,]  65     1         18                     17                     1
## [293,]  69     1         18                     11                     1
## [294,]  43     2         34                     19                     6
## [295,]  47     4         65                     14                    14
## [296,]  67     1         13                     10                     1
## [297,]  45     1         20                      1                     1
## [298,]  65     2         29                     11                     4
## [299,]  53     1         10                     21                     1
## [300,]  67     3         62                     13                     3
## [301,]  43     2         50                     18                     1
## [302,]  47     2         29                     23                     2
## [303,]  48     1         15                     30                     3
## [304,]  62     1         15                     46                    14
## [305,]  68     2         42                     25                     5
## [306,]  57     3        130                     10                    10
## [307,]  40     2         21                     22                     3
## [308,]  56     3         51                     10                     4
## [309,]  52     2         30                      4                     1
## [310,]  40     2         35                     19                     3
## [311,]  51     2         31                      4                     2
## [312,]  67     1         14                     15                     5
## [313,]  54     1         15                     14                     6
## [314,]  56     3         60                     27                    17
## [315,]  48     1         20                     12                     1
## [316,]  57     2         22                      4                     1
## [317,]  47     3         80                     14                     1
## [318,]  54     1         15                     14                     3
## [319,]  41     3        100                     28                    23
## [320,]  65     2         30                     12                     1
## [321,]  58     1          8                     18                     1
## [322,]  38     1         15                     15                     1
## [323,]  38     3         80                      8                     3
## [324,]  60     2         30                     19                     7
## [325,]  58     2         25                     16                     1
## [326,]  63     2         24                     15                     6
## [327,]  53     2         35                     14                     4
## [328,]  43     1         12                      1                     1
## [329,]  60     4         45                      9                     1
## [330,]  60     2         25                     10                     9
## [331,]  47     2         35                     24                     1
## [332,]  48     2         28                     19                     2
## [333,]  59     1         17                      6                     3
## [334,]  56     1         15                     19                     1
## [335,]  53     2         32                     13                     1
## [336,]  48     1         15                     11                     2
## [337,]  52     3         60                      4                     1
## [338,]  61     3         90                     13                     2
## [339,]  66     1         11                     19                     3
## [340,]  45     2         37                     13                     4
## [341,]  52     2         21                     12                     3
## [342,]  67     1          2                     19                     9
## [343,]  40     3         70                     17                     1
## [344,]  50     1          8                      9                     1
## [345,]  65     2         22                     23                     5
## [346,]  55     2         40                     12                    12
## [347,]  47     1         13                      5                     1
## [348,]  49     2         32                     16                     2
## [349,]  53     1          5                     29                     9
## [350,]  53     1         18                     17                     2
## [351,]  44     3         52                     24                     4
## [352,]  54     2         31                     16                     4
## [353,]  51     1         14                      6                     1
## [354,]  46     1          7                      7                     1
## [355,]  47     1         12                      1                     1
## [356,]  68     2         21                     18                     1
## [357,]  50     1         20                     23                     2
## [358,]  67     2         26                      5                     2
## [359,]  47     1         16                      3                     1
## [360,]  68     1         15                     20                     1
## [361,]  55     2         25                     10                     2
## [362,]  47     1         20                     23                     1
## [363,]  56     3         80                     24                     3
## [364,]  51     2         30                      2                     2
## [365,]  41     1         16                     11                     2
## [366,]  67     1         20                     16                     4
## [367,]  58     1         17                     19                     7
## [368,]  67     3        100                     25                     8
## [369,]  63     2         41                     14                     4
## [370,]  69     1         16                     12                     6
## [371,]  59     2         25                     30                    11
## [372,]  44     4        108                     16                    14
## [373,]  65     1         12                      2                     1
## [374,]  48     2         38                     24                     4
## [375,]  39     2         24                     26                    13
## [376,]  55     2         45                     14                    13
## [377,]  50     3         98                     14                    12
## [378,]  39     2         25                     16                     3
## [379,]  49     2         30                     18                     1
##        Survival Months
##   [1,]              60
##   [2,]              62
##   [3,]              75
##   [4,]              84
##   [5,]              50
##   [6,]              89
##   [7,]              54
##   [8,]              14
##   [9,]              70
##  [10,]              92
##  [11,]              64
##  [12,]              92
##  [13,]              56
##  [14,]              38
##  [15,]              64
##  [16,]              49
##  [17,]             105
##  [18,]              62
##  [19,]             107
##  [20,]              77
##  [21,]              81
##  [22,]              50
##  [23,]              78
##  [24,]             102
##  [25,]              98
##  [26,]              70
##  [27,]             102
##  [28,]              82
##  [29,]              64
##  [30,]              86
##  [31,]              52
##  [32,]              49
##  [33,]              90
##  [34,]              62
##  [35,]              31
##  [36,]              77
##  [37,]              37
##  [38,]             103
##  [39,]              82
##  [40,]             105
##  [41,]              42
##  [42,]              61
##  [43,]              86
##  [44,]              84
##  [45,]              63
##  [46,]              90
##  [47,]              39
##  [48,]              59
##  [49,]              82
##  [50,]              82
##  [51,]              71
##  [52,]              71
##  [53,]              86
##  [54,]              70
##  [55,]              74
##  [56,]              73
##  [57,]              91
##  [58,]             106
##  [59,]              73
##  [60,]              77
##  [61,]              80
##  [62,]              49
##  [63,]              78
##  [64,]              75
##  [65,]              60
##  [66,]             106
##  [67,]              44
##  [68,]              85
##  [69,]              79
##  [70,]              84
##  [71,]             104
##  [72,]              12
##  [73,]              52
##  [74,]              98
##  [75,]              85
##  [76,]              95
##  [77,]              79
##  [78,]             106
##  [79,]              81
##  [80,]              55
##  [81,]             101
##  [82,]              65
##  [83,]              72
##  [84,]              55
##  [85,]              65
##  [86,]              71
##  [87,]              82
##  [88,]              84
##  [89,]              95
##  [90,]              95
##  [91,]              91
##  [92,]              57
##  [93,]              87
##  [94,]              40
##  [95,]              91
##  [96,]              50
##  [97,]              25
##  [98,]              73
##  [99,]              63
## [100,]              50
## [101,]              54
## [102,]              73
## [103,]               8
## [104,]              53
## [105,]              65
## [106,]              58
## [107,]              24
## [108,]              64
## [109,]             106
## [110,]              61
## [111,]              66
## [112,]              79
## [113,]              74
## [114,]              69
## [115,]             103
## [116,]              52
## [117,]              93
## [118,]              94
## [119,]              91
## [120,]              57
## [121,]              94
## [122,]              79
## [123,]              62
## [124,]              86
## [125,]              49
## [126,]              14
## [127,]             100
## [128,]              50
## [129,]              79
## [130,]              77
## [131,]              50
## [132,]              73
## [133,]              96
## [134,]              87
## [135,]              41
## [136,]              54
## [137,]              84
## [138,]              67
## [139,]              53
## [140,]             104
## [141,]              86
## [142,]             102
## [143,]              50
## [144,]              42
## [145,]              52
## [146,]             107
## [147,]              92
## [148,]              52
## [149,]              69
## [150,]              82
## [151,]             101
## [152,]              64
## [153,]              55
## [154,]              98
## [155,]              56
## [156,]              91
## [157,]              51
## [158,]             102
## [159,]              71
## [160,]              13
## [161,]              11
## [162,]              53
## [163,]              82
## [164,]              89
## [165,]              56
## [166,]              54
## [167,]              72
## [168,]             102
## [169,]              51
## [170,]             100
## [171,]              62
## [172,]              73
## [173,]              84
## [174,]              87
## [175,]              96
## [176,]              74
## [177,]              47
## [178,]              77
## [179,]              55
## [180,]              64
## [181,]              93
## [182,]              74
## [183,]              23
## [184,]              60
## [185,]              85
## [186,]              86
## [187,]              81
## [188,]              71
## [189,]              90
## [190,]              79
## [191,]              60
## [192,]              89
## [193,]              66
## [194,]              84
## [195,]              55
## [196,]              50
## [197,]              55
## [198,]              98
## [199,]              53
## [200,]             103
## [201,]              77
## [202,]              63
## [203,]              45
## [204,]              25
## [205,]              68
## [206,]              53
## [207,]              91
## [208,]             105
## [209,]              76
## [210,]              94
## [211,]              71
## [212,]              15
## [213,]             106
## [214,]              56
## [215,]              56
## [216,]              16
## [217,]              31
## [218,]              85
## [219,]              62
## [220,]              23
## [221,]              24
## [222,]              50
## [223,]             107
## [224,]              76
## [225,]              87
## [226,]             101
## [227,]              60
## [228,]              66
## [229,]              53
## [230,]              93
## [231,]              90
## [232,]              59
## [233,]              58
## [234,]              68
## [235,]              94
## [236,]              72
## [237,]              53
## [238,]             103
## [239,]              16
## [240,]              77
## [241,]              49
## [242,]              99
## [243,]             107
## [244,]              81
## [245,]              87
## [246,]             103
## [247,]              96
## [248,]              40
## [249,]              78
## [250,]              92
## [251,]             106
## [252,]              54
## [253,]              85
## [254,]              69
## [255,]              51
## [256,]              93
## [257,]              76
## [258,]              58
## [259,]              79
## [260,]              63
## [261,]               7
## [262,]             104
## [263,]              74
## [264,]              67
## [265,]              98
## [266,]             100
## [267,]              58
## [268,]              61
## [269,]              45
## [270,]              48
## [271,]              40
## [272,]              57
## [273,]              42
## [274,]              76
## [275,]              55
## [276,]              68
## [277,]              49
## [278,]              16
## [279,]              99
## [280,]              88
## [281,]              87
## [282,]              60
## [283,]              34
## [284,]              92
## [285,]              65
## [286,]              23
## [287,]              50
## [288,]             107
## [289,]              92
## [290,]              51
## [291,]              92
## [292,]              61
## [293,]              50
## [294,]              95
## [295,]              97
## [296,]              65
## [297,]              81
## [298,]              81
## [299,]              92
## [300,]              53
## [301,]              91
## [302,]              49
## [303,]              61
## [304,]              74
## [305,]              48
## [306,]              37
## [307,]              75
## [308,]              57
## [309,]              81
## [310,]              56
## [311,]              73
## [312,]              53
## [313,]              68
## [314,]              94
## [315,]              88
## [316,]              79
## [317,]              63
## [318,]              74
## [319,]              57
## [320,]              53
## [321,]             104
## [322,]              57
## [323,]              63
## [324,]              90
## [325,]              73
## [326,]              94
## [327,]              98
## [328,]              74
## [329,]              89
## [330,]              89
## [331,]             100
## [332,]              16
## [333,]             107
## [334,]              70
## [335,]              68
## [336,]              81
## [337,]              67
## [338,]              67
## [339,]              97
## [340,]              60
## [341,]              86
## [342,]              75
## [343,]              59
## [344,]              87
## [345,]              75
## [346,]              72
## [347,]             102
## [348,]             101
## [349,]              68
## [350,]              80
## [351,]             104
## [352,]              61
## [353,]              41
## [354,]             100
## [355,]             105
## [356,]              57
## [357,]              59
## [358,]              54
## [359,]              76
## [360,]              82
## [361,]              53
## [362,]             102
## [363,]              47
## [364,]             100
## [365,]             107
## [366,]              73
## [367,]              91
## [368,]              92
## [369,]             107
## [370,]              85
## [371,]              89
## [372,]              71
## [373,]             102
## [374,]              49
## [375,]              59
## [376,]              90
## [377,]              57
## [378,]              85
## [379,]              86
drop(scale(new_Cancer,center=center, scale=scale)%*%Cancer_pca$rotation[,1])
##   [1] -1.493744354  0.426322428  1.694207768 -1.767583528  0.043714825
##   [6] -1.028534021 -1.338771984  0.406514411  4.993025728  1.937948477
##  [11] -1.756901401  1.296312778 -0.090142691 -0.076244034  1.004107956
##  [16] -1.005634503 -0.538374841  0.204445317 -0.419443766 -0.252782392
##  [21] -0.036353656  0.504291512 -0.618672209  1.459334722  0.693501261
##  [26]  1.342457422  2.475721782 -1.137184838 -0.082096727 -0.951459346
##  [31]  0.004306142 -1.358590305 -1.790419403 -0.908445651  1.245709794
##  [36] -1.439873416  0.636390371 -1.304428696 -0.097417933 -0.188925650
##  [41]  2.535953943 -1.364589888 -1.095258604  0.018958421 -1.483766860
##  [46]  0.803570710 -0.776759752 -1.440160549  0.550199236 -1.959716237
##  [51]  0.283946083  0.584420507  2.164109035  1.673683848 -1.630123732
##  [56] -1.450559221 -0.534036352 -0.354843129 -1.178588655 -1.248535425
##  [61] -0.944827480 -1.056029210 -0.473763736  1.681009012 -1.312786276
##  [66] -1.639877002  4.455166578 -0.707613499 -1.710632794 -1.171903123
##  [71]  3.302612150  2.121655213  0.528823585 -1.868775707  0.683905846
##  [76]  0.821006546 -0.499967072  0.056071716  0.099588612 -1.638985742
##  [81]  0.865297254 -1.545124764 -0.757282603 -1.494668798 -1.198962297
##  [86]  1.053228198  2.839883593  1.506058603 -1.539415867 -2.166532837
##  [91]  0.893002750 -0.677904182 -0.646604416  1.683330979 -1.509921397
##  [96] -0.135237286  0.027644129 -0.637273583  1.070049729 -0.455435814
## [101]  4.600390311 -0.787145836  0.655142324 -0.428540034 -0.110654721
## [106] -0.734249607  0.296584193 -1.410702952 -0.418905210  0.446752555
## [111] -1.134059417  1.181466882  1.830654533  0.454774207  0.864920996
## [116] -0.897625868  1.357865125 -0.915336154  0.094948933 -0.037442692
## [121] -0.703244230  1.727474232  1.839479021  0.275373090 -0.732974709
## [126] -0.921856464 -0.151799435 -1.471716143 -1.483838817 -0.899242135
## [131] -1.358439633  0.549771469 -1.825714544 -1.466418848  0.713759778
## [136]  0.095641779 -0.311491252 -0.482193479  1.024336162  2.074951928
## [141] -1.891283328 -0.768896963 -0.660225602  0.458314079  0.202499186
## [146] -0.635694229 -1.314850127  2.618727317 -1.867933212 -0.390204192
## [151] -1.169108179 -0.593384345 -1.153893444 -1.299586961 -1.312753509
## [156]  2.158951805 -0.888545794 -1.604599290 -0.695240701  1.698058938
## [161]  0.523091631 -1.639464234 -1.775434759 -1.300191877  0.127243391
## [166]  0.728909729 -0.691130861  4.057107584  0.065928057 -1.537449988
## [171]  0.005212931  1.307010016 -1.400091197 -1.914378275 -1.354059138
## [176]  1.278137221 -0.240072950 -1.192542565  1.517499402  0.419667049
## [181] -1.183491054 -0.049231716 -1.497163756  1.362728567  3.022520941
## [186] -0.646848816  0.841699831 -0.341629561  0.597265999 -1.161264597
## [191] -0.477014120 -2.115125949 -0.991130507 -0.707735717  3.115036491
## [196] -1.696392904  0.151090645  1.330786502  0.296675856 -0.422623151
## [201] -0.318075869 -0.085308348 -1.822877611  1.201683038 -1.807181645
## [206] -1.784093888 -0.078106596 -0.721328123 -0.483839459  0.663630444
## [211]  1.978468906  2.937647970 -0.086636710 -1.481813930  0.623006822
## [216]  1.991882118  0.744165906  0.641119818 -1.586401627  4.773395918
## [221]  2.921320323  0.503935335 -1.241990069 -0.133856941 -1.486223026
## [226] -0.762041381  2.005021660  1.814305601 -1.411373860 -0.324175998
## [231] -0.456860329 -1.210396528  0.367888943 -1.737267642 -1.509987525
## [236] -1.290446225  3.655612544  0.611276361  6.711875034 -1.281390399
## [241]  0.776720455  0.008347450 -0.958826089  1.609087788  0.543831815
## [246] -1.795501728 -2.078996209  0.486998129 -0.821657492 -1.398504155
## [251]  0.526594325  0.120809384 -0.289560811  2.350354264  2.529945185
## [256] -0.594294620 -1.406577585 -1.651971076  0.415871178 -0.286827613
## [261] -0.645411407 -0.628353063 -0.136446586 -1.777655604 -1.357302997
## [266] -1.150407815 -0.854919366  1.748954057 -0.738423976 -0.346935263
## [271]  2.611945346 -0.054669716  0.590763284 -0.771766282  0.287407340
## [276] -1.904210848  1.980934953  4.349982486 -1.601460087  1.110817200
## [281] -1.635586546 -0.910449829  0.979721615 -0.472435837  0.298128461
## [286]  0.876478490  0.030556752  0.489276289  1.167193218  5.639123713
## [291]  0.076038156 -1.306362503 -1.492629535  0.548191410  3.173294742
## [296] -1.711510331 -1.420928885 -0.397038374 -1.338159554  1.238726422
## [301]  0.476798036  0.451358041 -0.410664267  0.631511135  0.606275351
## [306]  3.760469200  0.283257978  1.205872572 -0.547890175  0.675442079
## [311] -0.347420655 -1.082694803 -0.809911038  2.814192996 -1.219216145
## [316] -0.839858529  1.906604890 -1.128786006  4.980287452 -0.396555408
## [321] -1.686147468 -0.771587552  2.121003409  0.183525269 -0.388480855
## [326] -0.270374270 -0.016309255 -1.509365115  1.128006246 -0.013678857
## [331]  0.134239505  0.543266130 -1.694510184 -1.177192240 -0.154704801
## [336] -1.222393212  0.985284375  1.845084419 -1.537001279  0.486580696
## [341] -0.381846642 -1.058469609  1.953784231 -1.632770525 -0.069211481
## [346]  0.924645953 -1.679627649 -0.138978457 -0.306354427 -1.082397105
## [351]  1.560087096  0.213890453 -1.243101129 -1.723673624 -1.845736715
## [356] -0.533908899 -0.621852817 -0.663822556 -1.464448793 -1.523194528
## [361] -0.249284791 -0.978278825  2.298810986 -0.641761160 -1.237501132
## [366] -1.157403928 -0.796933393  2.646899548 -0.178975454 -1.330874437
## [371]  0.785519987  4.528600634 -2.215387412  0.852816653  1.528575274
## [376]  1.052831636  3.308075529  0.145308323 -0.100434292
predict(Cancer_pca)[,1]
##   [1] -1.493744354  0.426322428  1.694207768 -1.767583528  0.043714825
##   [6] -1.028534021 -1.338771984  0.406514411  4.993025728  1.937948477
##  [11] -1.756901401  1.296312778 -0.090142691 -0.076244034  1.004107956
##  [16] -1.005634503 -0.538374841  0.204445317 -0.419443766 -0.252782392
##  [21] -0.036353656  0.504291512 -0.618672209  1.459334722  0.693501261
##  [26]  1.342457422  2.475721782 -1.137184838 -0.082096727 -0.951459346
##  [31]  0.004306142 -1.358590305 -1.790419403 -0.908445651  1.245709794
##  [36] -1.439873416  0.636390371 -1.304428696 -0.097417933 -0.188925650
##  [41]  2.535953943 -1.364589888 -1.095258604  0.018958421 -1.483766860
##  [46]  0.803570710 -0.776759752 -1.440160549  0.550199236 -1.959716237
##  [51]  0.283946083  0.584420507  2.164109035  1.673683848 -1.630123732
##  [56] -1.450559221 -0.534036352 -0.354843129 -1.178588655 -1.248535425
##  [61] -0.944827480 -1.056029210 -0.473763736  1.681009012 -1.312786276
##  [66] -1.639877002  4.455166578 -0.707613499 -1.710632794 -1.171903123
##  [71]  3.302612150  2.121655213  0.528823585 -1.868775707  0.683905846
##  [76]  0.821006546 -0.499967072  0.056071716  0.099588612 -1.638985742
##  [81]  0.865297254 -1.545124764 -0.757282603 -1.494668798 -1.198962297
##  [86]  1.053228198  2.839883593  1.506058603 -1.539415867 -2.166532837
##  [91]  0.893002750 -0.677904182 -0.646604416  1.683330979 -1.509921397
##  [96] -0.135237286  0.027644129 -0.637273583  1.070049729 -0.455435814
## [101]  4.600390311 -0.787145836  0.655142324 -0.428540034 -0.110654721
## [106] -0.734249607  0.296584193 -1.410702952 -0.418905210  0.446752555
## [111] -1.134059417  1.181466882  1.830654533  0.454774207  0.864920996
## [116] -0.897625868  1.357865125 -0.915336154  0.094948933 -0.037442692
## [121] -0.703244230  1.727474232  1.839479021  0.275373090 -0.732974709
## [126] -0.921856464 -0.151799435 -1.471716143 -1.483838817 -0.899242135
## [131] -1.358439633  0.549771469 -1.825714544 -1.466418848  0.713759778
## [136]  0.095641779 -0.311491252 -0.482193479  1.024336162  2.074951928
## [141] -1.891283328 -0.768896963 -0.660225602  0.458314079  0.202499186
## [146] -0.635694229 -1.314850127  2.618727317 -1.867933212 -0.390204192
## [151] -1.169108179 -0.593384345 -1.153893444 -1.299586961 -1.312753509
## [156]  2.158951805 -0.888545794 -1.604599290 -0.695240701  1.698058938
## [161]  0.523091631 -1.639464234 -1.775434759 -1.300191877  0.127243391
## [166]  0.728909729 -0.691130861  4.057107584  0.065928057 -1.537449988
## [171]  0.005212931  1.307010016 -1.400091197 -1.914378275 -1.354059138
## [176]  1.278137221 -0.240072950 -1.192542565  1.517499402  0.419667049
## [181] -1.183491054 -0.049231716 -1.497163756  1.362728567  3.022520941
## [186] -0.646848816  0.841699831 -0.341629561  0.597265999 -1.161264597
## [191] -0.477014120 -2.115125949 -0.991130507 -0.707735717  3.115036491
## [196] -1.696392904  0.151090645  1.330786502  0.296675856 -0.422623151
## [201] -0.318075869 -0.085308348 -1.822877611  1.201683038 -1.807181645
## [206] -1.784093888 -0.078106596 -0.721328123 -0.483839459  0.663630444
## [211]  1.978468906  2.937647970 -0.086636710 -1.481813930  0.623006822
## [216]  1.991882118  0.744165906  0.641119818 -1.586401627  4.773395918
## [221]  2.921320323  0.503935335 -1.241990069 -0.133856941 -1.486223026
## [226] -0.762041381  2.005021660  1.814305601 -1.411373860 -0.324175998
## [231] -0.456860329 -1.210396528  0.367888943 -1.737267642 -1.509987525
## [236] -1.290446225  3.655612544  0.611276361  6.711875034 -1.281390399
## [241]  0.776720455  0.008347450 -0.958826089  1.609087788  0.543831815
## [246] -1.795501728 -2.078996209  0.486998129 -0.821657492 -1.398504155
## [251]  0.526594325  0.120809384 -0.289560811  2.350354264  2.529945185
## [256] -0.594294620 -1.406577585 -1.651971076  0.415871178 -0.286827613
## [261] -0.645411407 -0.628353063 -0.136446586 -1.777655604 -1.357302997
## [266] -1.150407815 -0.854919366  1.748954057 -0.738423976 -0.346935263
## [271]  2.611945346 -0.054669716  0.590763284 -0.771766282  0.287407340
## [276] -1.904210848  1.980934953  4.349982486 -1.601460087  1.110817200
## [281] -1.635586546 -0.910449829  0.979721615 -0.472435837  0.298128461
## [286]  0.876478490  0.030556752  0.489276289  1.167193218  5.639123713
## [291]  0.076038156 -1.306362503 -1.492629535  0.548191410  3.173294742
## [296] -1.711510331 -1.420928885 -0.397038374 -1.338159554  1.238726422
## [301]  0.476798036  0.451358041 -0.410664267  0.631511135  0.606275351
## [306]  3.760469200  0.283257978  1.205872572 -0.547890175  0.675442079
## [311] -0.347420655 -1.082694803 -0.809911038  2.814192996 -1.219216145
## [316] -0.839858529  1.906604890 -1.128786006  4.980287452 -0.396555408
## [321] -1.686147468 -0.771587552  2.121003409  0.183525269 -0.388480855
## [326] -0.270374270 -0.016309255 -1.509365115  1.128006246 -0.013678857
## [331]  0.134239505  0.543266130 -1.694510184 -1.177192240 -0.154704801
## [336] -1.222393212  0.985284375  1.845084419 -1.537001279  0.486580696
## [341] -0.381846642 -1.058469609  1.953784231 -1.632770525 -0.069211481
## [346]  0.924645953 -1.679627649 -0.138978457 -0.306354427 -1.082397105
## [351]  1.560087096  0.213890453 -1.243101129 -1.723673624 -1.845736715
## [356] -0.533908899 -0.621852817 -0.663822556 -1.464448793 -1.523194528
## [361] -0.249284791 -0.978278825  2.298810986 -0.641761160 -1.237501132
## [366] -1.157403928 -0.796933393  2.646899548 -0.178975454 -1.330874437
## [371]  0.785519987  4.528600634 -2.215387412  0.852816653  1.528575274
## [376]  1.052831636  3.308075529  0.145308323 -0.100434292
#The aboved two gives us the same thing. predict is a good function to know.
Cancer$Survivor <- as.factor(Cancer$Survivor)
out <- sapply(1:5, function(i){plot(Cancer$Survivor,Cancer_pca$x[,i],xlab=paste("PC",i,sep=""),ylab="Survivor")})

pairs(Cancer_pca$x[,1:5], ylim = c(-6,4),xlim = c(-6,4),panel=function(x,y,...){text(x,y,Cancer$Survivor)})

# Better Ways to Visualize

library(factoextra)
## Welcome! Want to learn more? See two factoextra-related books at https://goo.gl/ve3WBa
library(FactoMineR)
library(ggfortify)
library(psych)
## 
## Attaching package: 'psych'
## 
## The following object is masked from 'package:car':
## 
##     logit
## 
## The following objects are masked from 'package:ggplot2':
## 
##     %+%, alpha
library(corrplot)
## corrplot 0.92 loaded
library(devtools)
## Loading required package: usethis
# Correlation
pairs.panels(Cancer[,-1],
             gap = 0,
             bg = c("red", "blue")[Cancer$Survivor],
             pch=21)

fviz_eig(Cancer_pca, addlabels = TRUE)

fviz_pca_var(Cancer_pca,col.var = "cos2",
             gradient.cols = c("#FFCC00", "#CC9933", "#660033", "#330033"),
             repel = TRUE)

fviz_pca_ind(Cancer_pca, col.ind = "cos2", 
                  gradient.cols = c("#FFCC00", "#CC9933", "#660033", "#330033"), 
                  repel = TRUE)

biplot(Cancer_pca)

autoplot(Cancer_pca,
         data = Cancer[,-1],
         loadings = TRUE,
         labels = Cancer$Survivor)

# Different PCA Method. 
res.pca <- PCA(Cancer[,-1], graph = FALSE)
print(res.pca)
## **Results for the Principal Component Analysis (PCA)**
## The analysis was performed on 379 individuals, described by 6 variables
## *The results are available in the following objects:
## 
##    name               description                          
## 1  "$eig"             "eigenvalues"                        
## 2  "$var"             "results for the variables"          
## 3  "$var$coord"       "coord. for the variables"           
## 4  "$var$cor"         "correlations variables - dimensions"
## 5  "$var$cos2"        "cos2 for the variables"             
## 6  "$var$contrib"     "contributions of the variables"     
## 7  "$ind"             "results for the individuals"        
## 8  "$ind$coord"       "coord. for the individuals"         
## 9  "$ind$cos2"        "cos2 for the individuals"           
## 10 "$ind$contrib"     "contributions of the individuals"   
## 11 "$call"            "summary statistics"                 
## 12 "$call$centre"     "mean of the variables"              
## 13 "$call$ecart.type" "standard error of the variables"    
## 14 "$call$row.w"      "weights for the individuals"        
## 15 "$call$col.w"      "weights for the variables"
# Visualize and Interpret PCA using these functions 

#get_eigenvalue(res.pca): Extract the eigenvalues/variances of principal components
#fviz_eig(res.pca): Visualize the eigenvalues
#get_pca_ind(res.pca), get_pca_var(res.pca): Extract the results for individuals and variables, respectively.
#fviz_pca_ind(res.pca), fviz_pca_var(res.pca): Visualize the results individuals and variables, respectively.
#fviz_pca_biplot(res.pca): Make a biplot of individuals and variables.

eig.val <- get_eigenvalue(res.pca)
eig.val
##       eigenvalue variance.percent cumulative.variance.percent
## Dim.1  2.2378787        37.297979                    37.29798
## Dim.2  1.1649997        19.416662                    56.71464
## Dim.3  0.9784385        16.307309                    73.02195
## Dim.4  0.9209868        15.349780                    88.37173
## Dim.5  0.5100636         8.501061                    96.87279
## Dim.6  0.1876326         3.127210                   100.00000
fviz_eig(res.pca, addlabels = TRUE, ylim = c(0, 50))

var <- get_pca_var(res.pca)

#var$coord: coordinates of variables to create a scatter plot
#var$cos2: represents the quality of representation for variables on the factor map. It’s calculated as the squared coordinates: var.cos2 = var.coord * var.coord.
#var$contrib: contains the contributions (in percentage) of the variables to the principal components. 
#The contribution of a variable (var) to a given principal component is (in percentage) : (var.cos2 * 100) / (total cos2 of the component).
var
## Principal Component Analysis Results for variables
##  ===================================================
##   Name       Description                                    
## 1 "$coord"   "Coordinates for the variables"                
## 2 "$cor"     "Correlations between variables and dimensions"
## 3 "$cos2"    "Cos2 for the variables"                       
## 4 "$contrib" "contributions of the variables"
# Coordinates
head(var$coord)
##                             Dim.1      Dim.2       Dim.3       Dim.4
## Age                    -0.3222059  0.2332281 -0.34538598  0.84965955
## Stage                   0.8420261 -0.3528792  0.06110566  0.23471133
## Tumor Size              0.8709647 -0.3046266 -0.01417789  0.20513599
## Regional Node Examined  0.3553161  0.8128074  0.20888379 -0.02009270
## Reginol Node Positive   0.6867038  0.4740946  0.01662008 -0.01753655
## Survival Months        -0.2620363 -0.0886666  0.90072386  0.31809437
##                              Dim.5
## Age                     0.02389842
## Stage                  -0.13460531
## Tumor Size             -0.09635083
## Regional Node Examined -0.41115983
## Reginol Node Positive   0.55012576
## Survival Months         0.10197883
# Cos2: quality on the factore map
head(var$cos2)
##                             Dim.1       Dim.2        Dim.3        Dim.4
## Age                    0.10381664 0.054395332 0.1192914718 0.7219213433
## Stage                  0.70900791 0.124523708 0.0037339019 0.0550894103
## Tumor Size             0.75857952 0.092797395 0.0002010125 0.0420807734
## Regional Node Examined 0.12624954 0.660655847 0.0436324379 0.0004037167
## Reginol Node Positive  0.47156209 0.224765673 0.0002762270 0.0003075306
## Survival Months        0.06866303 0.007861765 0.8113034757 0.1011840305
##                               Dim.5
## Age                    0.0005711344
## Stage                  0.0181185895
## Tumor Size             0.0092834832
## Regional Node Examined 0.1690524091
## Reginol Node Positive  0.3026383510
## Survival Months        0.0103996819
# Contributions to the principal components
head(var$contrib)
##                            Dim.1      Dim.2       Dim.3       Dim.4      Dim.5
## Age                     4.639064  4.6691283 12.19202521 78.38563371  0.1119732
## Stage                  31.682142 10.6887329  0.38161845  5.98156347  3.5522213
## Tumor Size             33.897258  7.9654435  0.02054421  4.56909623  1.8200637
## Regional Node Examined  5.641483 56.7086700  4.45939492  0.04383523 33.1433948
## Reginol Node Positive  21.071834 19.2931955  0.02823141  0.03339143 59.3334482
## Survival Months         3.068220  0.6748298 82.91818582 10.98647993  2.0388989
#The plot Below is also known as variable correlation plots. It shows the relationships between all variables. It can be interpreted as follow:

#Positively correlated variables are grouped together.
#Negatively correlated variables are positioned on opposite sides of the plot origin (opposed quadrants).
#The distance between variables and the origin measures the quality of the variables on the factor map. 
#Variables that are away from the origin are well represented on the factor map.

# Correlation circle
fviz_pca_var(res.pca, col.var = "black")

# Quality of representation


corrplot(var$cos2, is.corr=FALSE)

# Total cos2 of variables on Dim.1 and Dim.2
#A high cos2 indicates a good representation of the variable on the principal component. 
#In this case the variable is positioned close to the circumference of the correlation circle.
#A low cos2 indicates that the variable is not perfectly represented by the PCs. 
#In this case the variable is close to the center of the circle.

fviz_cos2(res.pca, choice = "var", axes = 1:2)

fviz_pca_var(res.pca, col.var = "cos2",
             gradient.cols = c("#00AFBB", "#E7B800", "#FC4E07"), 
             repel = TRUE # Avoid text overlapping
             )

# Change the transparency by cos2 values
fviz_pca_var(res.pca, alpha.var = "cos2")

corrplot(var$contrib, is.corr=FALSE)

# Contributions of variables to PC1
fviz_contrib(res.pca, choice = "var", axes = 1, top = 10)

# Contributions of variables to PC2

# Description of PC

res.desc <- dimdesc(res.pca, axes = c(1,2,3,4,5), proba = 0.05)
# Description of dimension 1
res.desc$Dim.1
## 
## Link between the variable and the continuous variables (R-square)
## =================================================================================
##                        correlation       p.value
## Tumor Size               0.8709647 2.118538e-118
## Stage                    0.8420261 4.258836e-103
## Reginol Node Positive    0.6867038  3.629109e-54
## Regional Node Examined   0.3553161  1.015769e-12
## Survival Months         -0.2620363  2.277214e-07
## Age                     -0.3222059  1.326702e-10
res.desc$Dim.2
## 
## Link between the variable and the continuous variables (R-square)
## =================================================================================
##                        correlation      p.value
## Regional Node Examined   0.8128074 1.692844e-90
## Reginol Node Positive    0.4740946 1.235575e-22
## Age                      0.2332281 4.455756e-06
## Tumor Size              -0.3046266 1.400911e-09
## Stage                   -0.3528792 1.483228e-12
res.desc$Dim.3
## 
## Link between the variable and the continuous variables (R-square)
## =================================================================================
##                        correlation       p.value
## Survival Months          0.9007239 1.380762e-138
## Regional Node Examined   0.2088838  4.160170e-05
## Age                     -0.3453860  4.655452e-12
res.desc$Dim.4
## 
## Link between the variable and the continuous variables (R-square)
## =================================================================================
##                 correlation       p.value
## Age               0.8496595 8.117074e-107
## Survival Months   0.3180944  2.334655e-10
## Stage             0.2347113  3.857241e-06
## Tumor Size        0.2051360  5.740140e-05
res.desc$Dim.5
## 
## Link between the variable and the continuous variables (R-square)
## =================================================================================
##                        correlation      p.value
## Reginol Node Positive    0.5501258 2.302831e-31
## Survival Months          0.1019788 4.726330e-02
## Stage                   -0.1346053 8.695976e-03
## Regional Node Examined  -0.4111598 6.817718e-17
# Graph of Indiviuals
ind <- get_pca_ind(res.pca)
ind
## Principal Component Analysis Results for individuals
##  ===================================================
##   Name       Description                       
## 1 "$coord"   "Coordinates for the individuals" 
## 2 "$cos2"    "Cos2 for the individuals"        
## 3 "$contrib" "contributions of the individuals"
## Principal Component Analysis Results for individuals
##  ===================================================
##   Name       Description                       
## 1 "$coord"   "Coordinates for the individuals" 
## 2 "$cos2"    "Cos2 for the individuals"        
## 3 "$contrib" "contributions of the individuals"
#To get access to the different components, use this:

# Coordinates of individuals
head(ind$coord)
##         Dim.1      Dim.2       Dim.3      Dim.4       Dim.5
## 1 -1.49571890  1.6749148 -0.79882567  0.6402257 -0.85340433
## 2  0.42688597 -0.1242504 -0.22240645 -0.4786708  0.01494530
## 3  1.69644730 -0.5458449  0.07002965  1.0340669  0.03911005
## 4 -1.76992006 -0.8864728 -0.03088789  0.2089963  0.77293051
## 5  0.04377261 -1.6055077 -0.90431537 -0.8507928  0.07847539
## 6 -1.02989362  0.5034039  0.86504682 -0.4218416 -0.23355708
# Quality of individuals
head(ind$cos2)
##          Dim.1      Dim.2       Dim.3       Dim.4        Dim.5
## 1 0.3274322470 0.41058866 0.093395406 0.059991224 0.1065936095
## 2 0.3729259505 0.03159324 0.101226350 0.468891786 0.0004570965
## 3 0.6732837945 0.06970372 0.001147311 0.250158183 0.0003578443
## 4 0.6695024705 0.16794832 0.000203902 0.009335167 0.1276808541
## 5 0.0004637016 0.62381877 0.197912619 0.175178687 0.0014903924
## 6 0.4290771448 0.10251416 0.302712164 0.071986248 0.0220666662
# Contributions of individuals
head(ind$contrib)
##          Dim.1       Dim.2        Dim.3      Dim.4        Dim.5
## 1 0.2637692749 0.635360823 0.1720803475 0.11742853 0.3767437880
## 2 0.0214856261 0.003496474 0.0133389606 0.06564190 0.0001155435
## 3 0.3393165082 0.067479762 0.0013224861 0.30634069 0.0007912489
## 4 0.3693444212 0.177977767 0.0002572787 0.01251367 0.3090418632
## 5 0.0002259067 0.583794159 0.2205296909 0.20737433 0.0031856891
## 6 0.1250572789 0.057394224 0.2017931729 0.05098076 0.0282177573
fviz_pca_ind(res.pca)

fviz_pca_ind(res.pca, col.ind = "cos2", 
             gradient.cols = c("#00AFBB", "#E7B800", "#FC4E07"),
             repel = TRUE # Avoid text overlapping (slow if many points)
             )

fviz_pca_ind(res.pca, pointsize = "cos2", 
             pointshape = 21, fill = "#E7B800",
             repel = TRUE # Avoid text overlapping (slow if many points)
             )

fviz_pca_ind(res.pca, col.ind = "cos2", pointsize = "cos2",
             gradient.cols = c("#00AFBB", "#E7B800", "#FC4E07"),
             repel = TRUE # Avoid text overlapping (slow if many points)
             )

fviz_cos2(res.pca, choice = "ind")

# Total contribution on PC1 and PC2
fviz_contrib(res.pca, choice = "ind", axes = 1:2)

# Create a random continuous variable of length 23,
# Same length as the number of active individuals in the PCA
set.seed(123)
my.cont.var <- rnorm(49)
# Color individuals by the continuous variable
fviz_pca_ind(res.pca,
             geom.ind = "point", # show points only (nbut not "text")
             col.ind = Cancer$Survivor, # color by groups
             palette = c("#00AFBB", "#E7B800", "#FC4E07"),
             addEllipses = TRUE, # Concentration ellipses
             legend.title = "Groups"
             )

fviz_pca_ind(res.pca, geom.ind = "point", col.ind = Cancer$Survivor, 
             palette = c("#00AFBB", "#E7B800", "#FC4E07"),
             addEllipses = TRUE, ellipse.type = "confidence",
             legend.title = "Groups"
             )

fviz_pca_ind(res.pca,
             label = "none", # hide individual labels
             habillage = Cancer$Survivor, # color by groups
             addEllipses = TRUE, # Concentration ellipses
             palette = "jco"
             )

fviz_pca_var(res.pca, geom.var = c("point", "text"))

# Show individuals text labels only
fviz_pca_ind(res.pca, geom.ind =  "text")

# Change the size of arrows an labels
fviz_pca_var(res.pca, arrowsize = 1, labelsize = 5, 
             repel = TRUE)

# Change points size, shape and fill color
# Change labelsize
fviz_pca_ind(res.pca, 
             pointsize = 3, pointshape = 21, fill = "lightblue",
             labelsize = 5, repel = TRUE)

fviz_pca_ind(res.pca,
             geom.ind = "point", # show points only (but not "text")
             group.ind = Cancer$Survivor, # color by groups
             legend.title = "Groups",
             mean.point = FALSE)

fviz_pca_ind(res.pca,
             geom.ind = "point", # show points only (but not "text")
             group.ind = Cancer$Survivor, # color by groups
             legend.title = "Groups",
             mean.point = TRUE)

fviz_pca_var(res.pca, axes.linetype = "blank")

ind.p <- fviz_pca_ind(res.pca, geom = "point", col.ind = Cancer$Survivor)
ggpubr::ggpar(ind.p,
              title = "Principal Component Analysis",
              subtitle = "Iris data set",
              caption = "Source: factoextra",
              xlab = "PC1", ylab = "PC2",
              legend.title = "Survivor", legend.position = "top",
              ggtheme = theme_gray(), palette = "jco"
              )

fviz_pca_biplot(res.pca, repel = TRUE,col.ind = Cancer$Survivor,
                col.var = "#2E9FDF", # Variables color
                )

fviz_pca_biplot(res.pca, 
                col.ind = Cancer$Survivor, palette = "jco", 
                addEllipses = TRUE, label = "var",
                col.var = "black", repel = TRUE,
                legend.title = "Survivorship") 

fviz_pca_biplot(res.pca, 
                # Fill individuals by groups
                geom.ind = "point",
                pointshape = 21,
                pointsize = 2.5,
                fill.ind = Cancer$Survivor,
                col.ind = "black",
                # Color variable by groups
                legend.title = list(fill = "Survivor", color = "Clusters"),
                repel = TRUE        # Avoid label overplotting
             )+
  ggpubr::fill_palette("jco")+      # Indiviual fill color
  ggpubr::color_palette("npg")      # Variable colors

fviz_pca_biplot(res.pca, 
                # Individuals
                geom.ind = "point",
                fill.ind = Cancer$Survivor, col.ind = "black",
                pointshape = 21, pointsize = 2,
                palette = "jco",
                addEllipses = TRUE,
                # Variables
                alpha.var ="contrib", col.var = "contrib",
                gradient.cols = "RdYlBu",
                
                legend.title = list(fill = "Survivor", color = "Contrib",
                                    alpha = "Contrib")
                )

# ANOVA
summary(aov(Cancer$Stage ~ Cancer$Survivor))
##                  Df Sum Sq Mean Sq F value   Pr(>F)    
## Cancer$Survivor   1   8.38   8.379   13.81 0.000233 ***
## Residuals       377 228.78   0.607                     
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
summary(aov(Cancer$Age ~ Cancer$Survivor))
##                  Df Sum Sq Mean Sq F value Pr(>F)
## Cancer$Survivor   1      5    4.91   0.058  0.809
## Residuals       377  31774   84.28
# MANOVA
summary(manova(as.matrix(Cancer[,-1])~ Cancer$Survivor))
##                  Df  Pillai approx F num Df den Df    Pr(>F)    
## Cancer$Survivor   1 0.27145     23.1      6    372 < 2.2e-16 ***
## Residuals       377                                             
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1